Forcably enable or disable disulfide detection. When unspecified, rosetta conservatively detects disulfides in full atom input based on SG distance, but will not form centroid disulfides. Setting '-detect_disulf true' will force aggressive disulfide detection in centroid poses based on CB distance. Setting '-detect_disulf false' disables all detection, even in full atom poses. Note that disabling disulfides causes severe clashes for native disulfides.

-detect_disulf_tolerance <Real>

disulf tolerance
Default: 0.5

-constraints_from_link_records <Boolean>

Turn link records into atom pair and angle constraints
Default: false

-auto_setup_metals <Boolean>

Automatically adds covalent linkages to bound metal ions, as well as atom pair constraints and angle constraints to hold ions in place, on PDB import. Also, sets the atom_pair_constraint and angle_constraint weights in the default score function to 1.0. False by default.
Default: false

-prevent_auto_setup_metal_bb_variants <Boolean>

When automatically setting up metals, in cases where there is a bond detected between a metal and a backbone heavyatom (e.g. a backbone carbonyl oxygen), by default Rosetta will set up bonded variant types for the current residue and for all orther residue types with an equivalent backbone heavyatom, to permit mutations. Setting this flag to true prevents this. False by default.
Default: false

-metals_detection_LJ_multiplier <Real>

When -auto_setup_metals is used, overlap between metal atoms and metal-binding atoms is used as the criterion by which covalent bonds are detected. The Lennard-Jones radii of the atoms can be multiplied by a constant factor in order to detect longer bonds to metal ions. Default 1.0.
Default: 1.0

-metals_distance_constraint_multiplier <Real>

Distances between metals and metal-binding atoms are constrained using harmonic potentials, scaled by this multiplier. Default 1.0. Set to 0.0 to skip adding distance constraints.
Default: 1.0

Specify the filename(s) of (a) *.codes files that includes a list of alternative 3-letter codes. The default directory is database/input_output/3-letter_codes/ but any path can be provided. Duplicate codes in successive files will overwrite previous ones.
Default: utility::vector1<std::string>(1,"default.codes")

-maintain_links <Boolean>

Maintains link records in the PDB when using auto_detect_glycans
Default: false

-fix_disulf <File>

Specify disulfide connectivity via a file. Disulfides are specified as two whitespace-separated residue indices per line. This option replaces the old '-run:fix_disulf' option.

-missing_density_to_jump <Boolean>

If missing density is found in input pdbs, replace with a jump
Default: false

-target_residues <IntegerVector>

which residue numbers to pass for getDistConstraints

-replonly_residues <IntegerVector>

residue numbers regarded as repulsive-only residues

-replonly_loops <Boolean>

all loops will be regarded as repulsive-only
Default: false

-use_database <Boolean>

Read in structures from database. Specify database via -inout:dbms:database_name and wanted structures with -in:file:tags or select_structures_from_database

-select_structures_from_database <StringVector>

specify an SQL query to determine which structures get read in from a database specified with -inout:dbms:database_name. SELECT query must return structures.tag

in:dbms

-dbms <Boolean>

dbms option group

-struct_ids <StringVector>

List of struct_ids (hex representation) to be used by the database job inputter

Create a chemical jump for each residue in these chains (String of 1-letter chain IDs)
Default: " "

-residue_type_set <String>

ResidueTypeSet for input files
Default: "fa_standard"

-pca <File>

compute PCA projections
Default: ""

-silent_energy_cut <Real>

energy cut for silent-files
Default: 1.0

-silent_list <FileVector>

Silent input filename list(s) - like -l is to -s

-silent_renumber <Boolean>

renumber decoys in not_universal_main or not
Default: false

-silent_struct_type <String>

Type of SilentStruct object to use in silent-file input
Default: "protein"

-silent_read_through_errors <Boolean>

will ignore decoys with errors and continue reading
Default: false

-silent_score_prefix <String>

Prefix that is appended to all scores read in from a silent-file
Default: ""

-silent_select_random <Integer>

Select a random subset of this number of decoys from every silent-file read
Default: 0

-silent_select_range_start <Integer>

Select a ranged subset of decoys from every silent-file read. Start at this decoy.
Default: -1

-silent_select_range_mul <Integer>

Select a blocksize multiplier. This param pasically multiplies -silent_select_range_start. E.g. when set to, say, 5, -silent_select_range_start 0,1,2,3,4 will result in decoys being read starting from 0,5,10,15,20
Default: 1

-silent_select_range_len <Integer>

Select a ranged subset of decoys from every silent-file read. Start at this decoy.
Default: 1

By default, CONECT information is written for all noncanonicals and HETATMs, except waters. If this flag is set to true, it will be written for ALL residues, subject to the distance cutoff (-inout:connect_info_cufoff) and overridden by -inout:skip_connect_info.
Default: false

-connect_info_cutoff <Real>

The atom separation cutoff above which bonded atoms have explicit CONECT records written so that programs like PyMOL know the atomic connectivity. Default 0.0 Angstroms (write all records).
Default: 0.0

Suppress use of tracer color codes, which can appear as '^[[0m' in log files
Default: false

-chname <Boolean>

Add Tracer chanel names to output
Default: true

-chtimestamp <Boolean>

Add timestamp to tracer channel name
Default: false

-dry_run <Boolean>

If set ComparingTracer will not generate any asserts, and save all Tracer output to a file
Default: false

-mpi_tracer_to_file <String>

MPI ONLY: Redirect all tracer output to this file with '<mpi_rank>' appened as a suffix
Default: "tracer.out"

-std_IO_exit_error_code <Integer>

Specify error code that will be used to exit if std::IO error detected. This is useful if you want to detect situations like: Rosetta output was redirected to a file but the disk got full, etc. Default value is 0 which means that error detection code is turned off.
Default: 0

Set whether or not ligands are output with unique chainIDs, even if they share a chainID with one of the peptide chains in the input structure. The default value is false.
Default: false

-output_virtual <Boolean>

Output virtual atoms in output of PDB
Default: false

-output_virtual_zero_occ <Boolean>

Set occupancy to 0.0 for virtual atoms in output of PDB
Default: false

-no_chainend_ter <Boolean>

If true, TER records are not written at the ends of chains in PDB files – only at the end of all of the ATOM records (the legacy Rosetta behaviour). False by default (which results in TER records at the ends of every chain).
Default: false

If the pose contains a comment named template, print this as a REMARK in the pdb file
Default: false

-per_chain_renumbering <Boolean>

When used in conjunction with renumber_pdb, restarts residue numbering at each chain.
Default: false

-output_secondary_structure <Boolean>

output HELIX and SHEET records to StructFileRep / PDB
Default: false

-do_not_autoassign_SS <Boolean>

Depends on -out:file:output_secondary_structure. If outputting SS, if this flag is true, it will NOT generate the secondary structure automatically; it will instead assume the secstruct string in the pose is correct
Default: false

-output_torsions <Boolean>

Output phi, psi, and omega torsions in the PDB output if the pose is ideal.
Default: false

If the pose contains any comment print it as a COMMENT in the pdb file.
Default: false

-force_nonideal_structure <Boolean>

Force ResidueConformationFeatures to treat the structure as nonideal. If you know all your structures are non-ideal this decreases pose output time
Default: true

-set_pdb_author <String>

Set the author name(s), if any, to output in the .pdb Title Section. List of names should be comma-delimited.
Default: ""

-write_pdb_title_section_records <Boolean>

Sets whether or not the title section records in PDB files are written. The title section includes HEADER, EXPDTA, AUTHOR, and REMARK records. The default value is true.
Default: true

-write_pdb_link_records <Boolean>

Sets whether or not the LINK records in PDB files are written. The default value is true.
Default: true

-use_pdb_format_HETNAM_records <Boolean>

Sets whether or not the HETNAM records in PDB files are written in the standard PDB format with a single record per 3-letter code. The default value is false, which means that the file will use the Rosetta format, which provides a unique HETNAM record for each residue.
Default: false

-write_pdb_parametric_info <Boolean>

If true, parametric poses have their parameter info included in the REMARK lines of the output PDB file. True by default.
Default: true

-write_glycan_pdb_codes <Boolean>

If true glycans will be written based on the pdb codes rather than the rosetta names
Default: false

-write_seqres_records <Boolean>

Sets whether or not the SEQRES records in PDB files are written. The default value is false.
Default: false

-output_pose_energies_table <Boolean>

Output the pose energies table. This can be overridden
Default: true

-output_pose_cache_data <Boolean>

Output the pose cache.
Default: true

-output_pose_fold_tree <Boolean>

Output the foldtree of the pose. Will go in rosetta_additional column for cif files.
Default: false

-output_only_asymmetric_unit <Boolean>

For symmetrical poses, de-symmetrize the pose before output in order to output only the master subunit. Energies will still be output as symmetrical. Does not work with Silent files.
Default: false

run MPIMultiCommJobDistributor with n_replica processes per job
Default: 1

-shuffle <Boolean>

Shuffle job order
Default: false

-n_cycles <Integer>

Option to control miscellaneous cycles within protocols. This has no core meaning - it is meant to reduce option-bloat by having every protocol define separate cycles options. Check your protocol's documentation to see if it is used.
Range: 1-
Default: 1

-repeat <Integer>

Repeat mover N times
Range: 0-
Default: 1

-max_min_iter <Integer>

Maximum number of iterations of dfpmin
Default: 200

-maxruntime <Integer>

Maximum runtime in seconds. JobDistributor will signal end if time is exceeded no matter how many jobs were finished.
Default: -1

-maxruntime_bufferfactor <Real>

If set, the JobDistributor will attempt to stop if there doesn't appear to be enough time for maxruntime_bufferfactor jobs before maxruntime occurs.
Default: 0

-write_failures <Boolean>

write failed structures to output
Default: false

-benchmark <Boolean>

Run in benchmark mode

-test_cycles <Boolean>

When running tests, use reduced cycles. Cycles must be defined in the code itself
Default: false

-memory_test_cycles <Boolean>

use together with test_cycles to keep number of copies of anything as high as in production mode
Default: false

-dry_run <Boolean>

Run through structures/tasks/etc skipping the actual calculation step for testing of I/O and/or setup
Default: false

-debug <Boolean>

Run in debug mode

-profile <Boolean>

Run in profile mode
Default: false

-max_retry_job <Integer>

If a job fails with FAIL_RETRY retry this many times at most
Default: 10

-version <Boolean>

write out detailed version info, if it was available at compile time
Default: false

calculate values of a series of additional structural properties, including counting unsatisfied buried Hbond donors and acceptors, SASApack, etc. Additional output associated with this flag is written both to stdout and to output PDB files

-output_hbond_info <Boolean>

print hydrogen bond info in the stats section of written out PDB files

This value will be added to the random number seed. Useful when using time as seed and submitting many jobs to clusters. Using the condor job id will force jobs that are started in the same second to still have different initial seeds
Default: 0

-rng <String>

Random number generation algorithm: Currently only mt19937 is a accepted here
Default: "mt19937"

-rebuild_disulf <Boolean>

Attempt to build correct disulfide geometry when converting from a centroid pose to a full atom pose. Disulfides must be previously annotated, either by enabling -detect_disulf or by specifying a file to -fix_disulf.
Default: false

-preserve_header <Boolean>

Maintain header info from input PDB when writing output PDBs

-suppress_checkpoints <Boolean>

Override & switch off checkpoints.

-checkpoint <Boolean>

Turn checkpointing on

-delete_checkpoints <Boolean>

delete the checkpoints after use
Default: true

-checkpoint_interval <Integer>

Checkpoint time interval in seconds
Range: 10-
Default: 600

-protocol <String>

Which protocol to run, for Rosetta wrapper
Default: "abrelax"

-remove_ss_length_screen <Boolean>

Sets the use_ss_length_screen flag in the Fragment Mover to false

-min_type <String>

type of minimizer to use
Default: "lbfgs_armijo_nonmonotone"

-min_tolerance <Real>

minimizer tolerance
Default: 0.000001

-nblist_autoupdate <Boolean>

Turn on neighborlist auto-updates for all minimizations
Default: false

-nblist_autoupdate_narrow <Real>

With nblist autoupdate: the reach in Angstroms for the narrow neighbor list
Default: 0.5

-nblist_autoupdate_wide <Real>

With nblist autoupdate: the reach in Angstroms for the wide neighbor list
Default: 2.0

-skip_set_reasonable_fold_tree <Boolean>

Do not run set_reasonable_fold_tree when creating a pose from a pdb. Useful for unreasonable PDBs where the user sets a fold tree explicitly.
Default: false

discard coords information for missing density atoms ( occupancy is zero ) defined in input structures. Default is to keep those coordinates because this is a consistent problem for end users
Default: true

write other_pose (JobOutputter) to a scorefile; path by other_pose_scorefile; be warned you can get garbage if scorefunctions for poses do not match. Overridden by no_scorefile
Default: false

-other_pose_scorefile <File>

Path to other_pose (JobOutputter) scorefiles. Default is same scorefile as regular result poses. The default will cause problems if your output poses were scored on different scorefunctions.
Default: ""

-intermediate_scorefiles <Boolean>

write intermediate evaluations to disk (depends on your protocol if and how often this happens
Default: false

Signal Rosetta is to be run as a library in an interactive application. In particular, favor throwing exceptions on bad inputs rather than exiting.
Default: false

-nosignal <Boolean>

Don't install the signal handler to catch segfaults, etc. in the crash reporter. Useful for running under a debugger.
Default: false

-crash_to_console <Boolean>

Show the backtrace on the console/tracer in addition to the crash report file.
Default: false

-condor <Boolean>

if condor say yes – proc_id counting starts at 0
Default: false

-nproc <Integer>

number of process... needed if proc_id is specified
Default: 0

-proc_id <Integer>

give process number... Jobdistributor will only work on proc_id mod nproc part of work
Default: 0

-exit_if_missing_heavy_atoms <Boolean>

quit if heavy atoms missing in pdb
Default: false

-show_simulation_in_pymol <Real>

Attach PyMOL observer to pose at the beginning of the simulation. Waits until at least every [argument] seconds before sending pose if something has changed, default 5. A value of 0 indicates to not skip any packets from sending! Don't forget to run the PyMOLPyRosettaServer.py script within PyMOL!
Default: 5.0

-update_pymol_on_energy_changes_only <Boolean>

Only Update the simulation in on energy change. Useful if pymol observer is segfaulting on length changes.
Default: false

-update_pymol_on_conformation_changes_only <Boolean>

Only update the simulation in pymol on conformation change.
Default: false

-keep_pymol_simulation_history <Boolean>

Keep history when using show_simulation_in_pymol flag?
Default: false

run:PyMOLMover

-PyMOLMover <Boolean>

PyMOLMover option group

-address <String>

TCP port address to use when initializing PyMOLMover
Default: ""

-port <Integer>

TCP port to use when initializing PyMOLMover
Default: 0

-max_packet_size <Integer>

Max size of packet to send to PyMOL. Default value is dependable from address: for 127.0.0.1 it will be set to 7678 and any other addresses to 1500.
Default: 0

parser

-parser <Boolean>

parser option group

-protocol <String>

The protocol you will be running. (Input XML File

-script_vars <StringVector>

Variable substitutions for xml parser, in the form of name=value

-view <Boolean>

Use the viewer?

-info <StringVector>

Have the rosetta_scripts application print out the available XML-accessible options for a given mover, filter, task operation, or residue selector, and then exit.

-output_schema <String>

Have the rosetta_scripts application write out its XML Schema to the given file and then exit.

-validate_and_exit <Boolean>

After XML Schema validation completes, exit

-patchdock <String>

Patchdock output file name.

-patchdock_random_entry <IntegerVector>

Pick a random patchdock entry between two entry numbers. inclusive

-inclusion_recursion_limit <Integer>

How many recursions to perform when parsing an XML file with inclusions
Default: 8

determine if we should use the WorkPartition job distributor
Default: false

-job_definition_schema <File>

If provided on the command line, the job distributor will write the XML Schema for the applciation's job definition file out to disk and then exit

-mpi_fast_nonblocking_output <Boolean>

By default the master node blocks while a slave node outputs to avoid two slaves writing to a score file or silent file at the same time setting this to true disables that feature
Default: false

-n_archive_nodes <Integer>

The number of nodes that should perform archival roles only. This flag is only used by the MPIWorkPoolJobDistributor
Default: 0

-do_not_archive_on_node0 <Boolean>

Should the master node in the MPIWorkPoolJobDistributor archive any JobResults on it? Only relevant for MPI builds when using -n_archive_nodes
Default: false

-mpi_fraction_outputters <Real>

Fraction of the MPI nodes that node0 is allowed to use to output job results; non-archive nodes that output will also perform regular work in addition to their output work. This flag should range from 0 to 1. Note that node0 never outputs, so even if this is set to 0, one node will be deputized as an output node.
Default: 0.01

-nthreads <Integer>

For the multithreaded job distributor, how many threads should be run at the same time

-archive_on_disk <String>

Sometimes job results use a ton of memory. This option tells Rosetta to store job results on disk instead of in memory. The string you pass here should be the name of a (preferably empty) directoy where we can put all of our temporary files. You can delete this directory and everything in it when Rosetta is done running.
Default: "null"

-compress_job_results <Boolean>

Sometimes job results use a ton of memory. This option tells Rosetta to compress all job results so they use less memory.
Default: true

-resource_definition_files <FileVector>

Specify all the resources to available for the jobs running.

-resource_definition_schema <File>

If provided on the command line, the job distributor will write the XML Schema for the applciation's resource definition file out to disk and then exit

-load_input_poses_only_once <Boolean>

If the same Pose is used as input to multiple jobs (which can only happen when a job definition file is provided, but the input poses come from the command line), then preserve those input poses in memory until they will not be used in any future jobs. This necessarily comes with an increased memory footprint and is likely undesireable if the number of jobs is large!

-checkpoint <Boolean>

Should we checkpoint job progress? Uses default values for checkpoint_period and checkpoint_directory

-checkpoint_period <Integer>

The approximate number of minutes between checkpoints. If this flag is provided by the user, then checkpointing will occurr, even if the -checkpoint flag is not on the command line.
Default: 30

-checkpoint_directory <String>

What directory should checkpoints be written to? If this flag is provided by the user, then checkpointing will occurr, even if the -checkpoint flag is not on the command line.
Default: "checkpoints"

-restore_from_checkpoint <Boolean>

Should the contents of the checkpoint directory be used to restart a previously run job that was interrupted before it could be completed? If this flag is not present on the command line when trying to rerun a previously-run but interrupted job, then Rosetta will not attempt to restore the job from the checkpoint file. This is to safeguard against accidentally restoring from a checkpoint generated by some other execution of the code.

-continue_past_failed_checkpoint_restoration <Boolean>

Should we keep going even if we could not restore from a checkpoint as requested? Use this if you are ok with possibly of starting over from the beginning, or if you expect to relaunch the job multiple times and want simply to use the same command line each time, including the first time you launch the job and there are no checkpoints yet to restore from.

-keep_all_checkpoints <Boolean>

Allow old checkpoint files to build up on disk. Cannot be combined with -archive_on_disk. Using this flag could use up a lot of disk space unncessarily. If this flag is not present on the command line, then previously created checkpoints will be deleted when the next checkpoints are created. Note that job distributor will delete the previous checkpoint by default after the next checkpoint is written to disk.

-keep_checkpoint <Integer>

Prevent the JobDistributor from deleting a particular checkpoint; perhaps useful if you are trying to debug an infrequent event and you want to restart from a particular checkpoint repeatedly without worrying that the JobDistributor will delete your starting point.

use lazy silent file reader in job distributor, read in a structure only when you need to
Default: false

-mpi_nowait_for_remaining_jobs <Boolean>

exit immediately (not graceful – not complete) if the last job has been sent out
Default: false

-mpi_timeout_factor <Real>

timeout is X times average job-completion time - set to 0 to switch off
Default: 0

-mpi_work_partition_job_distributor <Boolean>

determine if we should use the WorkPartition job distributor
Default: false

-mpi_file_buf_job_distributor <Boolean>

determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
Default: true

-mpi_filebuf_jobdistributor <Boolean>

same as mpi_file_buf_job_distributor but with more intuitive spacing... determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
Default: true

-mpi_fast_nonblocking_output <Boolean>

By default the master node blocks while a slave node outputs to avoid two slaves writing to a score file or silent file at the same time setting this to true disables that feature
Default: false

-input_empty_pose <Boolean>

Give the job distributor an empty pose.
Default: false

-dd_parser <Boolean>

determine whether to use the dock_design_parser
Default: false

-ntrials <Integer>

number of attempts at creating an output file for each nstruct. e.g., ntrials 3 and nstruct 10 would mean that each of 10 trajectories would attempt to write an output file 3 times and if unsuccessful would fail.
Default: 1

-generic_job_name <String>

job name when using GenericJobInputter (i.e. abinitio)
Default: "S"

-no_output <Boolean>

use NoOutputJobOutputter; do not store the pose after a run (no silent or scorefile)
Default: false

-enzdes_out <Boolean>

causes an enzdes-style scorefile (with information about catalytic res and some pose metric stuff ) to be written instead of the regular scorefile
Default: false

-buffer_silent_output <Integer>

write structures to silent-files in blocks of N structures to
Default: 1

Delete poses after they have been processed. For jobs that process a large number of structures, the memory consumed by old poses is wasteful. True by default, since there is no good reason to effectively leak memory.
Default: true

-checkpoint_file <File>

write/read nstruct-based checkpoint files to the desired filename.

-failed_job_exception <Boolean>

If JD2 encounters an error during job execution, raise an exception at the end of the run
Default: true

-max_nstruct_in_memory <Integer>

If nstruct is set higher than this number, JD2 will keep only this many jobs in memory in the jobs list at any given time (to keep the jobs list from filling up memory). As jobs complete, they will be deleted and the jobs list will be filled out with new jobs. This option is intended for exteremly large runs on systems like the Blue Gene/Q supercomputer. To disable this sort of memory management, set this option to 0.
Default: 1000000

-sequential_mpi_job_distribution <Boolean>

If specified, MPI versions of the JobDistributor send jobs to each slave in sequence (slave1, slave2, slave3 etc.). False by default. Note that this should NOT be used for production runs; it is intended only for regression tests in which non-sequential job distribution would result in stochastic variations.
Default: false

-grid_ensemble <Boolean>

Do an ensemble search where each input pdb is used for an ensemble based search. Instead of each in file outputting nstruct, we use the input files to generate a total nstruct across the inputs
Default: false

-seed_ensemble <Boolean>

Do an ensemble search as in grid_search, but randomly choose the seeds over the inputs. See seed_ensemble_weights to weight the inputs
Default: false

-seed_ensemble_weights <RealVector>

Specifiy weights for seeded ensemble. Must match number of inputs. See also: -seed_ensemble_weights_file

-seed_ensemble_weights_file <File>

A file specifying weights to use for each input structure. Two columns. basename with extension (or relative path or full path), weight

-HOSTNAME_in_jobname <Boolean>

Pre-prefixes job with $HOSTNAME env var; useful for determining which server a job came from. When running in k8s pods, makes jobs distinct if they are all 0001

view

-view <Boolean>

view option group

-show_virtual_residues <Boolean>

Show virtual residues?
Default: true

-single_glycan_color <Boolean>

Show glycans as a single color instead of default
Default: true

score

-score_pose_cutpoint_variants <Boolean>

Include cutpoint variants in the pose during linear chainbreak
Default: false

Number of symmetric Units in design for use with symE scoring
Default: -1

-symE_bonus <Real>

Energy bonus per match for use with symE scoring
Default: 0.0

-symmetric_gly_tables <Boolean>

If true, the Ramachandran and P_AA_PP tables for glycine will be symmetrized on load. If false (the default), then the statistical tables will be used, which are asymmetric due to the contribution of chiral amino acids.
Default: false

When using occ_sol_exact with the exact_occ_pairwise flag, split the energies between both contributing residues instead of assigning it just to the polar residue (not recommended - intended for parameterization / evaluation purposes)
Default: false

-exact_occ_self_res_no_occ <Boolean>

Setting this to false means that the self-residue CAN occlude when using the exact ODO model, leading to potential double-counting with the Dunbrack energy but better results in loop discrimination.
Default: false

-exact_occ_radius_scaling <Real>

When using occ_sol_exact, scale the radii of occluding atoms by this factor (intended for parameterization / evaluation purposes)
Default: 1.0

The pro_close term holds the proline ring closed, but also has some inter-residue energy associated with the psi value of the preceding residue. If this flag is set to 'true', the term ONLY does the torsional stuff – it doesn't hold the ring closed. For use with cart_bonded or ring_close. False by default.
Default: false

-ring_close_shadow_constraint <Real>

Standard deviation of the harmonic potential used to hold shadow atoms atop real atoms in order to hold rings closed with the ring_close scoring term. Analogous to pro_close_planar_constraint option for the pro_close energy term.
Default: 0.1

-linear_bonded_potential <Boolean>

use linear (instead of quadratic) bonded potential
Default: false

-free_side_chain_bonus <Real>

Amount to reward virtualization of a protein side chain, per free chi
Default: -0.5

-compute_mg_sol_for_hydrogens <Boolean>

mg_sol includes penalties for hydrogens near Mg(2+)
Default: false

-rg_local_span <IntegerVector>

First,last res in rg_local. For example to calc rg_local from 1-20 would be 1,20
Default: 0

intermolecular concentration to use in intermol term (give in M)
Default: 1.0

-sidechain_buried <IntegerVector>

count buried residues (rvernon pilot app)
Default: -1

-sidechain_exposed <IntegerVector>

count exposed residues (rvernon pilot app)
Default: -1

-aa_composition_setup_file <StringVector>

The filename of one or more setup files for the aa_composition scoring term. (Multiple such files can be listed, separated by a space.) The default location for these files (which have a .comp extension) is /database/scoring/score_functions/aa_composition/.

-aa_repeat_energy_penalty_file <String>

The filename of a penalty file for the aa_repeat_energy term. The penalty file should be a series of numbers on a single line, representing the penalty for having a repeat of 1, 2, 3, etc. of the same residue. Penalty files are stored in database/scoring/score_functions/aa_repeat_energy/ and should have the suffix .rpt_pen. The default is default_repeat_penalty_table.rpt_pen.
Default: "default_repeat_penalty_table.rpt_pen"

-approximate_buried_unsat_penalty_hbond_energy_threshold <Real>

Energy threshold for a h-bond to be considered satisfying a buried polar. Should be a negative number. (Setting to -0.001 will be much faster than 0 at runtime)
Default: -0.25

-approximate_buried_unsat_penalty_burial_atomic_depth <Real>

The atomic depth cutoff to determine whether or not a polar atom is buried. Measured from the Sasa surface.
Default: 4.5f

Should we assume that the backbone atoms will not change during a packing trajectory? (i.e. no positions that include normal aa and proline or n-methyl) If set to false, this energy method takes longer to compute. (~ 2X as long)
Default: true

The hbnet score term's bonus function can scale in different ways as the size of a network grows. The default is quadratic growth, though linear, logarithmic, and square root growth are all allowed.
Default: "quadratic"

-hbnet_max_network_size <Integer>

This is the maximum hydrogen bond network size, beyond which the hbnet score term will not give any more bonus. Defaults to 0, which means no limit.
Default: 0

The filename of one or more setup files for the netcharge scoring term. (Multiple such files can be listed, separated by a space.) The default location for these files (which have a .charge extension) is /database/scoring/score_functions/netcharge/.

-mhc_epitope_setup_file <StringVector>

The filename of one or more setup files for the mhc_epitope scoring term. (Multiple such files can be listed, separated by a space.) The default location for these files (which have a .mhc extension) is /database/scoring/score_functions/mhc_epitope/.

slope for burial measure calc from lnPF for HRF_MSlabeling score term
Default: 3.827

-ms_fit_intercept <Real>

intercept for burial measure calc from lnPF for HRF_MSlabeling score term
Default: 36.202

-ms_fade_outer <Real>

outer limit for FadeFunc in HRF_MSLabeling score term
Default: 10.0

-ms_fade_dist <Real>

fade distance for FadeFunc in HRF_MSLabeling score term
Default: 5.0

-nmer_ref_energies <String>

nmer ref energies database filename

-nmer_ref_energies_list <String>

list of nmer ref energies database filenames

-nmer_pssm <String>

nmer pssm database filename

-nmer_pssm_list <String>

list of nmer pssm database filenames

-nmer_pssm_scorecut <Real>

nmer pssm scorecut gate for ignoring lowscore nmers
Default: 0.0

-nmer_svm <String>

nmer svm filename (libsvm)
Default: ""

-nmer_svm_list <String>

list of nmer svm filenames (libsvm)
Default: ""

-nmer_svm_rank <String>

nmer svm rank scores filename (libsvm)
Default: ""

-nmer_svm_rank_list <String>

list of nmer svm rank scores filenames (libsvm)
Default: ""

-nmer_svm_scorecut <Real>

nmer svm scorecut gate for ignoring lowscore nmers
Default: 0.0

-nmer_svm_aa_matrix <String>

nmer svm sequence encoding matrix filename

-nmer_svm_term_length <Integer>

how many up/dnstream res to avg and incl in svm sequence encoding
Default: 3

-nmer_svm_pssm_feat <Boolean>

add pssm features to svm encoding?
Default: true

-nmer_svm_avg_rank_as_energy <Boolean>

use average of svm score ranks as rsd energy for NmerSVM scoring method, good for normalizing across mhc/hla alleles
Default: false

-nmer_ref_seq_length <Integer>

length of nmers in nmer_ref score
Default: 9

-just_calc_rmsd <Boolean>

In rna_score, just calculate rmsd – do not replace score.
Default: false

-envsmooth_zero_negatives <Boolean>

use alternative envsmooth table with a floor of 0.0 (envsmooth awards no energy bonus)
Default: false

-rama_power <Real>

If rama > 0.0, raise to the nth power. This has been useful for Foldit design. Note that this creates derivative discontinuities, so it should be used with caution! If not specified, the default rama behaviour (no power function) is preserved.
Default: 1.0

-ideal_sugars <Boolean>

Triggers loading of only the ideal chair conformations of sugars with 6 member rings.
Default: false

-hbond_fade <Real>

fade_factor for hbond geometry softmax
Default: 2.5

-hbond_new_sp3_acc <Boolean>

fade_factor for hbond geometry softmax
Default: false

-alignment_sharpness <Real>

When computing a harmonic function of RMSD for the alignment score, what should the standard deviation be?
Default: 1.0

For the arg_cation_pi scoreterm. Can histidine be the pi-side of an Arginine cation-pi interaction?
Default: true

-mc_optimize_dG <Boolean>

Optimize the dG during MonteCarlo. It is not possible to do this within overall scoring, but where possible, do this during MC calls. This option does not globally-use the MonteCarloInterface object, but is protocol-specific. This is due to needing to know the interface it will be used on. dG is measured by the InterfaceAnalyzerMover. Supported Code is currently RosettaAntibodyDesign and RosettaDock
Default: false

-mc_interface_weight <Real>

Weight of interface score if using MonteCarloInterface with a particular protocol.
Default: 1.0

-mc_total_weight <Real>

Weight of total score if using MonteCarloInterface with a particular protocol
Default: 0.0

-force_sugar_bb_zero <Boolean>

Force the SugarBB weight to be zero from get_score_function. When using include_sugars, the sugar_bb weight is automatically added. This overrides that for benchmarking purposes
Default: false

-voids_penalty_energy_containing_cones_cutoff <Integer>

A parameter for the voids_penalty score term. The minimum number of cones projecting from side-chains in which a voxel must lie in order for that voxel to be considerd to be buried. Defaults to 6 cones.
Default: 6

-voids_penalty_energy_cone_dotproduct_cutoff <Real>

A parameter for the voids_penalty score term. The cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector.
Default: 0.1

-voids_penalty_energy_cone_distance_cutoff <Real>

A parameter for the voids_penalty score term. The cutoff value for the distance from the cone base at which we are considered no longer to be within the cone. Defaults to 8.0 Angstroms.
Default: 8.0

-voids_penalty_energy_disabled_except_during_packing <Boolean>

If true, then the voids_penalty term is only evaluated during packing (and not scoring or minimizing). If false, then it is evaluated during packing and scoring (but not minimizing). True by default. Can be overridden for a particular ScoreFunction on a per-instance basis.
Default: true

-voids_penalty_energy_voxel_size <Real>

The size, in Angstroms, of the voxels used in the voxel grid for the voids_penalty energy. Defaults to 0.5 A (a cube with a side of 0.5 Angstroms).
Default: 0.5

-voids_penalty_energy_voxel_grid_padding <Real>

A parameter for the voids_penalty energy. This is the enlargement (on all sides) of the bounding box for the pose when setting up the voxel grid. Defaults to 1.0 A padding on all sides.
Default: 1.0

score:rna

-rna <Boolean>

rna option group

-rna_base_pair_xy_filename <String>

File name where the RNA pase pair XY potential is defined
Default: "scoring/rna/rna_base_pair_xy.dat"

-disable_orientation_dependent_rna_ch_o_bonds <Boolean>

Do not use orientation-dependent potential for RNA carbon hydrogen bonds
Default: false

multithreading

-multithreading <Boolean>

multithreading option group

-total_threads <Integer>

The number of threads to launch in the global thread pool. All thread-parallelized work will be distributed over these threads. The default is to launch 1 thread per process. Setting this to 0 means that all available threads will be used in the multithreaded build. The default (single-threaded) build only ever uses 1 thread. IMPORTANT: TO TAKE ADVANTAGE OF MULTI-THREADING, YOU MUST BUILD WITH extras=cxx11thead, AND YOU MUST SET THIS TO A VALUE OTHER THAN 1. Values greater than about 4 result in diminishing returns on performance.
Default: 1

-interaction_graph_threads <Integer>

The number of threads that the packer will request by default when calculating the interaction graph. This option is only used in the multi-threaded (extras=cxx11thread) build of Rosetta. Note that the total number of threads must be set with the -multi_threading:total_threads option. A given packing job may be assigned fewer threads than the number requested, depending on availability. Protocols may also override the default request. The default (0) means that all available threads will be used.
Default: 0

Turn on quasisymmetric packing using when using RotamerLinks
Default: false

-ndruns <Integer>

Number of fixbb packing iterations. Each time packing occurs, it will pack this many times and return only the best result. Implemented at level of PackRotamersMover.
Range: 1-
Default: 1

-soft_rep_design <Boolean>

Use larger LJ radii for softer potential

-mainchain_h_rebuild_threshold <Real>

Cutoff for rebuilding mainchain hydrogens during rotamer generation during packing. If the position of the hydrogen is less than the threshold from its ideal position, it is not rebuilt. Default 0.75 A.
Default: 0.75

-use_electrostatic_repulsion <Boolean>

Use electrostatic repulsion

-dump_rotamer_sets <Boolean>

Output NMR-style PDB's with the rotamer sets used during packing
Default: false

-dunbrack_prob_buried <Real>

fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'buried' residues RotamericSingleResidueDunbrackLibrary
Range: 0-1
Default: 0.98

-dunbrack_prob_nonburied <Real>

fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'nonburied' residues RotamericSingleResidueDunbrackLibrary
Range: 0-1
Default: 0.95

-dunbrack_prob_buried_semi <Real>

fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'buried' residues in SemiRotamericSingleResidueDunbrackLibrary
Range: 0-1
Default: 0.95

-dunbrack_prob_nonburied_semi <Real>

fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'nonburied' residues in SemiRotamericSingleResidueDunbrackLibrary
Range: 0-1
Default: 0.87

-no_optH <Boolean>

Do not optimize hydrogen placement at the time of a PDB load
Default: true

-optH_MCA <Boolean>

If running optH, use the Multi-Cool Annealer (more consistent, but slower)
Default: false

seqpos numbers of his residus whose tautomer should be fixed during repacking
Default: []

-print_pymol_selection <Boolean>

include pymol-style selections when printing a PackerTask
Default: false

-extrachi_cutoff <Integer>

number of neighbors a residue must have before extra rotamers are used. default: 18
Default: 18

-resfile <FileVector>

resfile filename(s). Most protocols use only the first and will ignore the rest; it does not track against -s or -l automatically.
Default: ['"resfile"']

-sc_branch_rotamers <Boolean>

construct rotamers for conjugated side chains. Warning: results in deformation of the conjugation bond length and angles, so should be followed by some correction
Default: ['false']

-outeriterations_scaling <Real>

Multiplier for number of outer iterations
Default: 1.0

-inneriterations_scaling <Real>

Multiplier for number of inner iterations
Default: 1.0

-adducts <StringVector>

Gives list of adduct names to generate for residue definitions. Each adduct name may be followed by an optional integer, which gives a maximum number of adducts of that type which will be generated.

-use_input_sc <Boolean>

Use rotamers from input structure in packing By default, input sidechain coords are NOT included in rotamer set but are discarded before the initial pack; with this flag, the the input rotamers will NOT be discarded. Note that once the starting rotamers are replaced by any mechanism, they are no longer included in the rotamer set (rotamers included by coordinates)

-unboundrot <FileVector>

Read 'native' rotamers from supplied PDB(s). Unlike -use_input_sc, these rotamers will not be lost during repacks. This option requires specific support from the protocol; it is NOT built in to PackerTask.initialize_from_command_line()

-max_rotbump_energy <Real>

discard rotamers with poor interactions with the background using the specified cutoff. Values must be in the range of 0 to 5.0.
Default: 5.0

-lazy_ig <Boolean>

Force the packer to always allocate pair energy storage but procrastinate energy caclulation until each RPE is needed; each RPE is computed at most once. Memory use is quadratic in rotamers per residue. The InteractionGraphFactory will prefer the linear-memory interaction graph to the Lazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
Default: false

-double_lazy_ig <Boolean>

Force the packer to always procrastinate allocation AND energy caclulation until each RPE is needed; each RPE is computed at most once. The InteractionGraphFactory will prefer the linear-memory interaction graph to the DoubleLazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
Default: false

-linmem_ig <Integer>

Force the packer to use the linear memory interaction graph; each RPE may be computed more than once, but recently-computed RPEs are reused. The integer parameter specifies the number of recent rotamers to store RPEs for. 10 is the recommended size. Memory use scales linearly with the number of rotamers at about 200 bytes per rotamer per recent rotamers to store RPEs for (~4 KB per rotamer by default)
Default: 10

-precompute_ig <Boolean>

Explicitly request the O(N^2) interaction graph that precopmutes all 2-body energies. This option is overriden by linmem_ig.
Default: false

-multi_cool_annealer <Integer>

Alternate annealer for packing. Runs multiple quence cycles in a first cooling stage, and tracks the N best network states it observes. It then runs low-temperature rotamer substitutions with repeated quenching starting from each of these N best network states. 10 is recommended.

-sequence_symmetric_annealer <Boolean>

When used, the packer will enforce that all chains end up with the same sequence. It uses pdb info to link residues together, so all residues with the same pdb number will be the same amino acid in the end. If a residue does not have a partner on every chain, it will not be allowed to mutate. Like traditional symmetry, this assumes that all chains are part of the same symmetric system. It is impossible to have, say, chains A+B+C where A+B are symmetric and C is separate.
Default: false

-smart_annealer <Boolean>

(requires extras=tensorflow) Use AI to guide your packing protocol. Currently not usable with the multi_cool_annealer, but it may be soon.
Default: false

-smart_annealer_model <String>

(requires extras=tensorflow) Choose which neural network to use for the smart annealer. Look at database/protocol_data/tensorflow_graphs/smart_annealer/ to see the options. Passing this flag enables '-smart_annealer'
Default: "jack3.07.1"

-smart_annealer_cutoff <Real>

(requires extras=tensorflow) Choose a number from 0 to 1 to tune how aggressive the smart annealer is. Higher numbers are more agressive (risky) but have a potentially greater speedup (speedup requires -smart_annealer_pick_again false). Passing this flag enables '-smart_annealer'
Default: 0.25

-smart_annealer_pick_again <Boolean>

(requires extras=tensorflow) If disabled, the smart annealer just skips unfruitful amino acids. Enabling this option tells the annealer to pick a fruitful rotamer to sample this round instead of skipping the round. Will not give you a speedup but may give you a better final outcome. Passing this flag enables '-smart_annealer'
Default: true

-smart_annealer_disable_during_quench <Boolean>

(requires extras=tensorflow) Run the final quenching stage as normal, regardless of how bad an amino acid may be. Passing this flag enables '-smart_annealer'
Default: true

-minpack_temp_schedule <RealVector>

Alternate annealing schedule for min_pack.

-minpack_inner_iteration_scale <Integer>

The number of inner iterations per rotamer to run at each temperature in min pack.

-minpack_disable_bumpcheck <Boolean>

Disable bump check in min pack (i.e. include rotamers that collide with the background.

packing:ex1

-ex1 <Boolean>

use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff

packing:exdna

packing:packer_palette

-packer_palette <Boolean>

packer_palette option group

-extra_base_type_file <File>

PackerPalettes define the set of residue types with which one is designing, and TaskOperations allow types to be turned off at specific positinos. The default PackerPalette includes the twenty canonical amino acids. If this option is used to provide a file containing a whitespace-separated list of residue type names, the default PackerPalette will include these additional residue types.

-NCAA_expanded <Boolean>

Design positions like beta-AAs, oligoureas, and polyaramids with a default set of options

carbohydrates

-carbohydrates <Boolean>

carbohydrates option group

-glycam_pdb_format <Boolean>

Indicates that the input PDB files were generated by GLYCAM and thus join any HO- or RO- "residues" to the following one since Rosetta is smart enough to patch reducing ends. The default value is false.
Default: false

-linkage_conformer_data_file <String>

Specify the file where glycosidic linkage conformer torsion angle statistical data is stored. The default directory is database/chemical/carbohydrates/linkage_conformers/but any path can be provided. The default filename is default.table
Default: "default.table"

carbohydrates:glycan_sampler

-glycan_sampler <Boolean>

glycan_sampler option group

-glycan_sampler_test <Boolean>

Indicates to go into testing mode for Glycan Relax. Will try all torsions in a given PDB in a linear fashion
Default: false

-glycan_sampler_rounds <Integer>

Number of rounds to use for Glycan Relax. Total rounds is this # times number of glycan residues in movemap
Default: 100

-min_rings <Boolean>

Minimize Carbohydrate Rings during minimization? Otherwise, we keep them at their input values (which is recommended).
Default: false

-final_min_glycans <Boolean>

Do a final minimization of glycans after glycan relax protocol?
Default: true

-glycan_sampler_movie <Boolean>

Make a movie of accepts and trials (send to pymol)
Default: false

-glycan_sampler_kt <Real>

KT for GlycanRelaxMover
Default: 2.0

-glycan_sampler_refine <Boolean>

Set the protocol to not start from a random conformation, and instead refine the structure.
Default: false

-cartmin <Boolean>

Use Cartesian-space minimization instead of dihedral
Default: false

-tree_based_min_pack <Boolean>

Use a random-tree based method to minimize and pack instead of minimizing and packing all of them during the randommover selection. This makes the speed of the algorithm mostly-linear with the addition of more glycans, and wastes less time packing and minimizing
Default: true

-population_based_conformer_sampling <Boolean>

Use the populations of the conformers as probabilities during our linkage conformer sampling. This makes it harder to overcome energy barriers with more-rare conformers
Default: false

-use_gaussian_sampling <Boolean>

Set whether to build conformer torsions using a gaussian of the angle or through uniform sampling up to 1 SD (default)
Default: true

NOT CURRENTLY USED. Distance for CB distance clash check. Residue is clashing if at least 1 atom is less than this distance

-ignore_hydrogens <Boolean>

Should we calculate only heavy-heavy atom clashes?
Default: false

-ignore_full_res_output <Boolean>

Should we output each glycan residue clash information in scorefile? Ignoring will make scorefile a bit smaller.
Default: false

-output_per_glycan_data <Boolean>

Should we output per glycan branch data? Easy to compute later on if full res output is on.
Default: false

rings

-rings <Boolean>

rings option group

-ring_conformer_dbpath <File>

Path to ring conformers in the Rosetta DB
Default: "chemical/ring_conformer_sets"

-lock_rings <Boolean>

Sets whether or not alternative ring conformations will be sampled by the protocol, (e.g, ring flips or puckering). Only low-energy conformers will be sampled, if known. Otherwise, all ideal ring conformers will be sampled. The default value is false.
Default: false

-idealize_rings <Boolean>

Sets whether or not the ring conformations of input poses are idealized (set to the lowest-energy ring conformer, according to the toplogy file for that residue). The default is false: the input ring conformations will be used.
Default: false

-sample_high_energy_conformers <Boolean>

Sets whether or not even ring conformations that are energy energy maxima will be sampled by the protocol. The default value is false; however, if the low energy ring conformers are not listed in the topology files, all ideal ring conformers will be sampled anyway.
Default: false

chemical

-chemical <Boolean>

chemical option group

-exclude_patches <StringVector>

Names of the residue-type-set patches which should not be applied; if you know which patches you do not need for a particular run, this flag can reduce your memory use

-include_patches <StringVector>

Names of the residue-type-set patches which should be applied even if excluded/commented out in patches.txt; useful for testing non-default patches

-add_atom_type_set_parameters <StringVector>

Additional AtomTypeSet extra-parameter files that should be read; format is a sequence of paired strings: <atom-type-set-tag1> <filename1> <atom-type-set-tag2> <filename2> ...

-add_mm_atom_type_set_parameters <StringVector>

Additional MMAtomTypeSet extra-parameter files that should be read; format is a sequence of paired string: <mm-atom-type-set-tag1> <filename1> <mm-atom-type-set-tag2> <filename2> ...

Modify atomic charge from the command line. Happens at time of params file reading, so changes will propagate to patched versions of the residue type. Format is: -chemical:set_atomic_charge <rsd-type-set1-name>:<rsd-type1-name>:<atom1-name>:<new-charge> <rsd-type-set2-name>:<rsd-type2-name>:<atom2-name>:<new-charge> ... For example: '-chemical:set_atomic_charge fa_standard:ARG:NE:-1'

-set_patch_atomic_charge <StringVector>

Modify patch atomic charge from the command line. Happens at time of patch file reading, so changes will propagate to patched versions of the residue type. Uses a simplified version of the residue selector so will probably not work for patches with complex selector logic. format should be:: -chemical:set_patch_atomic_charge <rsd-type-set1-name>:<rsd-type1-name>:<patch-name>:<atom1-name>:<new-charge> ... For example: '-chemical:set_atomic_charge fa_standard:PRO:NtermProteinFull:1H:-1'

turn on default corrections:See src/core/init/score_function_corrections.cc. Note that this is a flag for the older score12 scorefunction, which should NOT be used with talaris2013, talaris2014, ref2015, or the beta scorefunctions.
Default: false

If true, then canonical amino acids use Voronoi-style detection of neareset rotamer wells during fa_dun scoring instead of hard-coded rotamer well definitions. False by default (i.e. hard-coded definitions are used by defaults).
Default: false

-fa_dun_noncanonicals_use_voronoi <Boolean>

If true, then noncanonical amino acids and other polymer building blocks use Voronoi-style detection of neareset rotamer wells during fa_dun scoring instead of hard-coded rotamer well definitions. True by default (i.e. Voronoi-style detection is used by default). Setting this to false creates problems with many noncanonicals that have rotamer wells that aren't simple gauche+/gauche-/anti wells.
Default: true

-fa_dun_correct_rotamer_well_order <Boolean>

If true, the rotamer well order for rotamer files is corrected automatically to the Rosetta convention of lowest to highest in the range [0,360). False by default.
Default: false

-fa_dun_correct_achiral_peptoid_libraries <Boolean>

If true, the rotamer libraries for peptoids with achiral side-chains are symmetrized (so that mirror-image conformatoins score identically). Rotamer library generation can produce slight asymmetries, so this is an easy way around that problem. True by default.
Default: true

-no_his_his_pairE <Boolean>

Set pair term for His-His to zero

-no_his_DE_pairE <Boolean>

Set pair term for His-Glu and His-Asp to zero

-p_aa_pp <String>

Name of scoring/score_functions/P_AA_pp/P_AA_PP potential file (search in the local directory first, then look in the database)
Default: "scoring/score_functions/P_AA_pp/P_AA_pp"

-p_aa_pp_nogridshift <Boolean>

the format of p_aa_pp changed from using i*10+5 (5, 15, etc) to i*10 (0,10,etc.) as grid points

-rama_not_squared <Boolean>

Rama potential calculated as input for both rama and rama2b. By default, the potential is square for (ram a+entropy) > 1.0

Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency. Lazily loaded; for sampling only.
Default: "scoring/score_functions/rama/flat/avg_L_rama_str.dat"

-rama_map_sym_average_L_flat_stringent <File>

Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
Default: "scoring/score_functions/rama/flat/sym_all_rama_str.dat"

-rama_map_sym_gly_flat_stringent <File>

Ramachandran map for glycine, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
Default: "scoring/score_functions/rama/flat/sym_G_rama_str.dat"

-rama_map_sym_pro_flat_stringent <File>

Ramachandran map for proline, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
Default: "scoring/score_functions/rama/flat/sym_P_rama_str.dat"

Use the 2010 Dunbrack library instead of either the the 2002 library.
Default: true

-dun10_dir <String>

Name of dun10 dir
Default: "rotamer/ExtendedOpt1-5"

-dun02_file <String>

Name of dun02 input file
Default: "rotamer/bbdep02.May.sortlib"

-ch_o_bond_potential <String>

Name of ch_o_bond potential file (search in the local directory first, then look in the database)
Default: "scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat"

-lj_hbond_hdis <Real>

Lennard Jones sigma value for hatms, classically it's been at 1.95 but the average A-H distance for hydrogen bonding is 1.75 from crystal structures. (momeara)
Default: 1.75

-lj_hbond_OH_donor_dis <Real>

Lennard Jones sigma value for O in OH donor groups. Classically it has been 3.0 but the average distances from crystal structurs is 2.6 (momeara)
Default: 2.6

-score12prime <Boolean>

Restore to score funciton parameters to score12 parameters and have getScoreFuntion return with score12prime.wts. The score12prime.wts differs from standard.wts + score12.wts_patch, in that the reference energies have been optimized with optE for sequence profile recovery
Default: false

-hbond_energy_shift <Real>

The shift upwards (through addition) of the well depth for the hydrogen bond polynomials; this shift is applied before the weights are applied.
Default: 0.0

-hb_sp2_BAH180_rise <Real>

The rise from -0.5 for the BAH=180 value for the additive chi/BAH sp2 potential
Default: 0.75

-hb_sp2_outer_width <Real>

The width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). Use 0.357 in conjunction with the hb_energy_fade flag.
Default: 0.357

If true, then the BAH angle for sp3 (aka hydroxyl) acceptors is measured donor-hydrogen–acceptor-heavyatom–heavyatom-base instead of donor-hydrogen–accptor-heavyatom–hydroxyl-hydrogen
Default: true

-hb_fade_energy <Boolean>

Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function.
Default: true

-hb_exclude_ether_oxygens <Boolean>

no H-bonds to nucleic acid ether oxygens O3', O4', O5'
Default: false

-hb_cen_soft <Boolean>

Use softer version of cen_hb term
Default: false

-use_bicubic_interpolation <Boolean>

Instead of using bilinear interpolation to evaluate the Ramachandran, P_AA_pp and Dunbrack potentials, use bicubic interpolation. Avoids pile-ups at the grid boundaries where discontinuities in the derivatives frustrate the minimizer
Default: true

corrections:chemical

-chemical <Boolean>

chemical option group

-icoor_05_2009 <Boolean>

New set of idealized coordinates for full atom, 05-2009

-parse_charge <Boolean>

Use PARSE charge set.

-expand_st_chi2sampling <Boolean>

Ugly temporary hack. Expand the chi2 sampling for serine and threonine in the fa_standard residue type set so that samples are taken every 20 degrees (instead of every 60 degrees. This will soon be changed in the SER and THR params files themselves. This flag can be used with any residue type set (including the pre-s fa_standard version, and with the fa_standard_05.2009_icoor version) but is unncessary for the talaris2013 version (currently named fa_standard) as the expanded SER and THR sampling is already encoded in .params files for these two residues
Default: false

corrections

-shapovalov_lib_fixes_enable <Boolean>

Apply new code by Maxim Shapovalov from Dunbrack Lab such as for reading/using dun, rama, prop libraries in new format and options for applying different bug fixes. False value will employ old libraries and old code.
Default: true

New Ramachandran file in the new format used by rama
Default: "scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb"

-shap_rama_nogridshift <Boolean>

With correct flag there is a bug. Rama09_noEH_kernel25_it08.dat is used where prob values are reported exactly at the 10-deg grid while Rama_smooth_dyn.dat_ss_6.4 has values reported in the middle of bins. There is no need for 5-deg shift for newer Rama maps with values reported at the grid.
Default: true

Stepsize (in degrees) of rotatable waters when wat_axis_sampling is used
Default: 15.0

-include_vrt <Boolean>

allow for water virtualization
Default: true

enzymes

-enzymes <Boolean>

enzymes option group

-species <String>

Setting the species name limits the behavior of the simulated enzyme(s) used in this protocol to reactions known to occur in the given species. A species name must be in the format "e_coli" or "h_sapiens", (note the underscores,) which must also correspond to a directory in the Rosetta database, e.g., "database/virtual_enzymes/<enzyme_family>/h_sapiens/".
Default: "h_sapiens"

-enzyme <String>

If set, the simulated enzyme used in this protocol will use specific enzymatic details for this reaction from the database. If the species name has not been set, a "generic" enzyme from general family used in this protocol is assumed. An enzyme name must be as listed in an appropriate enzyme file in "database/virtual_enzymes/<enzyme_family>/<species_name_>/".
Default: "generic"

-efficiency <Real>

If set, the simulated enzyme used in this protocol will have the efficiency indicated, where 1.00 is 100%. A virtual enzyme with an efficiency of 0.50 will perform its reaction any given site 50% of the time. If not set, the value given in the database for this enzyme will be used. Enzyme efficiency data are found in "database/virtual_enzymes/<enzyme_family>/<species_name_>/".

evaluation

-evaluation <Boolean>

evaluation option group

-rmsd_target <FileVector>

[vector] determine rmsd against this/these structure(s)

-rmsd_column <StringVector>

[vector] use xxx as column name: rms_xxx

-rmsd_select <FileVector>

[vector] a bunch of loop files which makes rmsds with tags: rms_XXX, where XXX is basename of file

Should we perform rotamer trials and minimization after every KIC move but only within the loops:neighbor_dist of the residues in the moved KIC segment. Useful to speed up when using very large loop definitions (like when whole chains are used for ensemble generation).
Default: false

-max_kic_build_attempts <Integer>

Number of attempts at initial kinematic closure loop building
Default: 10000

-remodel_kic_attempts <Integer>

Number of kic attempts per inner cycle during perturb_kic protocol
Default: 300

apply torsion-restricted sampling, and derive the torsion string from the native [or, if not provided, starting] structure
Default: false

-always_remodel_full_loop <Boolean>

always remodel the full loop segment (i.e. the outer pivots are always loop start & end) – currently this only applies to the perturb stage – EXPERIMENTAL
Default: false

-taboo_sampling <Boolean>

enhance diversity in KIC sampling by pre-generating different torsion bins and sampling within those – this flag activates Taboo sampling in the perturb stage
Default: false

-taboo_in_fa <Boolean>

enhance diversity in KIC sampling by pre-generating different torsion bins and sampling within those – this flag activates Taboo sampling in the first half of the full-atom stage; use in combination with -loops:taboo_sampling or -kic_leave_centroid_after_initial_closure
Default: false

-ramp_fa_rep <Boolean>

ramp the weight of fa_rep over outer cycles in refinement
Default: false

-ramp_rama <Boolean>

ramp the weight of rama over outer cycles in refinement
Default: false

list of residues where the rotamers are kept fixed
Default: "keep_natro"

-refine_design_iterations <Integer>

iterations of refine and design
Default: 1

loops:ccd

-ccd <Boolean>

ccd option group

-max_rama_score_increase <Real>

Maximum increase in Ramachandran score that will be tolerated.
Default: 2.0

-max_torsion_delta_per_move <RealVector>

Maxmimum absolute torsion deviation for a single residue in a given move. Different deviations for residues in helical, extended or coil conformations must be supplied (in that order).
Default: ['1.0', '5.0', '10.0']

-max_torsion_delta <RealVector>

Maxmimum absolute torsion deviation for a single residue over the entire CCD closure. Different deviations for residues in helical, extended or coil conformations must be supplied (in that order).
Default: ['10.0', '50.0', '75.0']

-tolerance <Real>

Maximum RMSD (in Angstroms) of the duplicated atoms across the cutpoint that will be considered a successful closure.
Default: 0.08

-max_cycles <Integer>

Maximum number of CCD iterations to attempt. CCD will stop if the loop is closed in fewer cycles than the maximum.
Default: 100

mistakes

-mistakes <Boolean>

mistakes option group

-restore_pre_talaris_2013_behavior <Boolean>

Restore the set of defaults that were in place before the Talaris2013 parameters were made default. This is an umbrella flag and sets the following flags if they are not set on the command line to some other value -mistakes::chemical::pre_talaris2013_geometries true -corrections::score::dun10 false -corrections::score::use_bicubic_interpolation false -correctionsscore:hb_sp2_chipen false -corrections::score::hb_fade_energy false -corrections::score::hbond_measure_sp3acc_BAH_from_hvy false -corrections::score::lj_hbond_hdis 1.95 -corrections::score::lj_hbond_OH_donor_dis 3.0 -corrections::chemical::expand_st_chi2sampling false -score::weights pre_talaris_2013_standard.wts -score::patch score12.wts_patch -score::analytic_etable_evaluation false -score::hbond_params score12_params -score::smooth_fa_elec false -score::elec_min_dis 1.5 -chemical::set_atom_properties fa_standard:ONH2:LK_DGFREE:-10.0 fa_standard:NH2O:LK_DGFREE:-10.0 fa_standard:Narg:LK_DGFREE:-11.0 fa_standard:OH:LK_DGFREE:-6.77
Default: false

mistakes:chemical

-chemical <Boolean>

chemical option group

-pre_talaris2013_geometries <Boolean>

Use the version of the fa_standard geometries that were active before the Talaris2013 parameters were taken as default
Default: false

sasa

-sasa <Boolean>

sasa option group

-method <String>

The method used to calculate sasa. More will hopefully be added in the future.
Default: "LeGrand"

-include_hydrogens_explicitly <Boolean>

Include hydrogens explicitly in the calculation. Explicit vs implicit calculations use different radii sets. These default sets can be controlled via cmd line. Historically, calculations included hydrogens implicitly. Some protocols may overwrite this setting to their needs.
Default: true

-probe_radius <Real>

Probe radius used by SasaCalc. Default is radius of water. 1.2 is also commonly used.
Default: 1.4

-include_probe_radius_in_atom_radii <Boolean>

This is typically done in calculation of SASA, and in fact is one of the defining features of SASA. Turn this off to calculate the Surface Area instead.
Default: true

-include_only_C_S_in_hsasa <Boolean>

Include only carbon or sulfer in hsasa calculation. This is typical. Only revert to false if excluding polar atoms by charge or everything will be counted as hydrophobic. Note hydrogens are dealt with automatically.
Default: true

-exclude_polar_atoms_by_charge_in_hsasa <Boolean>

Polar carbons and other atoms should not be included in hydrophobic hSASA - though historically they were. Set this to false to get historic hsasa
Default: false

-polar_charge_cutoff <Real>

Charge cutoff (abs value) to use on heavy atoms if excluding hydrophobic atoms from hSASA calculation by charge. The default is optimized for protein atom types (which excludes only carbonyl and carboxyl carbons. By default only carbon and sulfer are excluded.
Default: .4

-implicit_hydrogen_radii_set <String>

The radii set to use when including hydrogens implicitly instead of explicitly. Chothia 1976 radii are used by the program Naccess. chothia=naccess
Default: "chothia"

-explicit_hydrogen_radii_set <String>

The radii set to use when including hydrogens explicitly. Default is reduce, which was generally agreed upon at Minicon 2014 and come from original data from Bondi (1964) and Gavezzotti (1983) . LJ are the Rosetta leonard-jones radii, which are not quite exactly from Charmm. Legacy radii were optimized for a no-longer-in-Rosetta scoreterm (Jerry Tsai et al 2003)
Default: "reduce"

allow anchor&jump to move; anchor held in place via constraints - you must specify constraints!
Default: false

-delete_interface_native_sidechains <Boolean>

benchmarking option. delete input sidechains as prepacking step before running centroid or fullatom phases. use if also using use_input_sc and doing benchmarking. use_input_sc is used because of sidechain minimization, not to maintain input sidechains.

-RMSD_only_this <File>

Perform only RMSD calculations without modifying input. Only used for re-running metrics during benchmarking/debugging.

-anchor_noise_constraints_mode <Boolean>

Hold the anchor loosely (via constraints), not rigidly. Automatically generate the constraints from the starting pose. Mildly randomize the anchor's placement before modeling (up to 1 angstrom in x,y,z from initial placement.) Only compatible with single-residue anchors. Used to meet a reviewer's commentary.
Default: false

-super_secret_fixed_interface_mode <Boolean>

hold the anchor-containing loop fixed. Currently in testing.
Default: false

Type of light chain if known. Only used for design for now.
Default: "unknown"

-check_cdr_chainbreaks <Boolean>

Check CDRs of input antibody for chainbreaks upon initializing RosettaAntibody and RosettaAntibodyDesign. Chainbreaks found will result in the model not proceeding. A peptide bond in the loop is considered broken if its C-N bond is > 2.0 A
Default: true

-check_cdr_pep_bond_geom <Boolean>

Check CDRs of input antibody for bad peptide bond geometry. This checks Ca-C-N and C-N-Ca bond angles for -large- deviations from the min max values found in a recent analysis of protein geometry - Conformation dependence of backbone geometry in proteins. Structure -. If found, the model will not proceed. Use FastRelax with bond angle min to fix issues. These issues usually arise from poorly resolved crystal loops or incorrectly solved structures. Many older antibody structures have some of these issues.
Default: false

Use CDR Dihedral cluster-based constraints which have the means as the actual cluster means. Setting this to false will use constraints that have the means set as cluster center data.
Default: true

-force_use_of_cluster_csts_with_outliers <Boolean>

Force the use of cluster dihedral constraints to use ones with outliers.
Default: false

-cluster_csts_stats_cutoff <Integer>

Value for cluster-based dihedral csts -> general dihedral csts switch. If number of total structures used for cluster-based constraints is less than this value, general dihedral constraints will be used. More data = better predictability.
Default: 10

-general_dihedral_cst_phi_sd <Real>

Standard deviation to use for phi while using general dihedral circular harmonic constraints
Default: 16.0

-general_dihedral_cst_psi_sd <Real>

Standard deviation to use for psi while using general dihedral circular harmonic constraints
Default: 16.0

-allow_omega_mismatches_for_north_clusters <Boolean>

Skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.
Default: false

-prefix <String>

Base/dir name prefix for antibody grafting output, split on /. By default this is grafting/.
Default: "grafting/"

-grafting_database <String>

Path to the Antibody Grafting Database from Rosetta tools repository. By default this option is empty and grafting_database is looked at ../../tools/antibody and then $ROSETTA/tools/antibody
Default: ""

-blastp <String>

Path to NCBI-Blast+ executable
Default: "blastp"

-exclude_pdbs <StringVector>

do not use given pdb(s) as sources for grafting (no default), e.g. 1ABC 2CDE

Force the use the Antibody Database with data from the North clustering paper. This is included in Rosetta. If a newer antibody database is not found, we will use this. The full ab db is available at http://dunbrack2.fccc.edu/PyIgClassify/
Default: false

-paper_ab_db_path <String>

Path to the North paper ab_db path. Only used if -paper_ab_db option is passed
Default: "/sampling/antibodies/antibody_database_rosetta_design_north_paper.db"

-seq_design_cdrs <StringVector>

Enable these CDRs for Sequence-Design. (Can be set here or in the instructions file. Overrides any set in instructions file if given)

-graft_design_cdrs <StringVector>

Enable these CDRs for Graft-Design. (Can be set here or in the instructions file. Overrides any set in instructions file if given)

-primary_cdrs <StringVector>

Manually set the CDRs which can be chosen in the outer cycle. Normally, we pick any that are sequence or graft -designing.

-mintype <String>

The default mintype for all CDRs. Individual CDRs may be set via the instructions file
Default: "min"

-disallow_aa <StringVector>

Disallow certain amino acids while sequence-designing (could still be in the graft-designed sequence, however). Useful for optimizing without, for example, cysteines and prolines. Applies to all sequence design profiles and residues from any region (cdrs, framework, antigen). You can control this per-cdr (or only for the CDRs) through the CDR-instruction file. A resfile is also accepted if you wish to limit specific positions directly.

-top_designs <Integer>

Number of top designs to keep (ensemble). These will be written to a PDB and each move onto the next step in the protocol.
Default: 1

-high_mem_mode <Boolean>

If false, we load the CDRSet (CDRs loaded from the database that could be grafted) on-the-fly for a CDR if it has more than 50 graft-design members. If true, then we cache the CDRSet before the start of the protocol. Typically, this will really only to come into play when designing all CDRs. For de-novo design of 5/6 CDRs, without limiting the CDRSet in the instructions file, you will need 3-4 gb per process for this option.
Default: false

-cdr_set_cache_limit <Integer>

If high_mem_mode is false, this is the limit of CDRSet cacheing we do before we begin load them on-the-fly instead. If high_mem_mode is true, then we ignore this setting. If you have extremely low memory per-process, lower this number
Default: 300

-design_protocol <String>

Set the main protocol to use. Note that deterministic is currently only available for the grafting of one CDR.
Default: "even_cluster_mc"

-run_relax <Boolean>

Run Dualspace Relax on each ensemble after designing (after snugdock if run). Also output pre-relaxed structures
Default: false

-run_interface_analyzer <Boolean>

Run the Interface Analyzer and add the information to the resulting score function for each top design output.
Default: true

-paratope <StringVector>

Use these CDRs as the paratope. Default is all of them. Currently only used for constraints. Note that these site constraints are only used during docking unless -enable_full_protocol_atom_pair_cst is set.

-epitope <StringVector>

Use these residues as the antigen epitope. Default is to auto-identify them within the set interface distance at protocol start if epitope constraints are enabled. Currently only used for constraints. PDB Numbering. Optional insertion code. Example: 1A 1B 1B:A. Note that these site constraints are only used during docking unless -enable_full_protocol_atom_pair_cst is set.
Default: []

-use_epitope_constraints <Boolean>

Enable use of epitope constraints to add SiteConstraints between the epitope and paratope. Note that paratope constraints are always used. Note that these site constraints are only used during docking unless -global_atom_pair_cst_scoring is set.
Default: false

-dihedral_cst_weight <Real>

Weight to use for CDR CircularHarmonic cluster-based or general constraints that are automatically added to each structure and updated after each graft. Set to zero if you dont want to use these constraints. Note that they are not used for the backrub mintype. Overrides weight/patch settings.
Default: .3

-atom_pair_cst_weight <Real>

Weight to use for Epitope/Paratope SiteConstraints. Paratope Side contraints are always used. Set to zero to completely abbrogate these constraints. Overrides weight/patch settings.
Default: 0.01

-global_dihedral_cst_scoring <Boolean>

Use the dihedral cst score throughout the protocol, including final scoring of the poses instead of just during minimization step
Default: false

-global_atom_pair_cst_scoring <Boolean>

Use the atom pair cst score throughout the protocol, including final scoring of the poses instead of just during docking. Typically, the scoreterm is set to zero for scorefxns other than docking to decrease bias via loop lengths, relax, etc. It may indeed help to target a particular epitope quicker during monte carlo design if epitope constraints are in use, as well for filtering final models on score towards a particular epitope if docking.
Default: true

-do_dock <Boolean>

Run a short lowres + highres docking step in the inner cycles. (dock/min). Recommended 2 inner cycles for better coverage. (dock/min/dock/min). Inner/Outer loops for highres are hard coded, while low-res can be changed through regular low_res options. If sequence design is enabled, will design regions/CDRs set during the high-res dock. Recommended to
Default: false

-outer_cycle_rounds <Integer>

Rounds for outer loop of the protocol (not for deterministic_graft ). Each round chooses a CDR and designs. One run of 100 cycles with relax takes about 12 hours. If you decrease this number, you will decrease your run time significantly, but your final decoys will be higher energy. Make sure to increase the total number of output structures (nstruct) if you use lower than this number. Typically about 500 - 1000 nstruct is more than sufficient. Full DeNovo design will require significantly more rounds and nstruct. If you are docking, runs take about 30 percent longer.
Default: 25

-inner_cycle_rounds <Integer>

Number of times to run the inner minimization protocol after each graft. Higher (2-3) rounds recommended for pack/min/backrub mintypes or if including dock in the protocol.
Default: 1

-dock_cycle_rounds <Integer>

Number of rounds for any docking. If you are seeing badly docked structures, increase this value.
Default: 1

Include outlier data for GraftDesign, profile-based sequence design stats, and cluster-based dihedral constraints. Outliers are defined as having a dihedral distance of > 40 degrees and an RMSD of >1.5 A to the cluster center. Use to increase sampling of small or rare clusters.
Default: false

-use_H3_graft_outliers <Boolean>

Include outliers when grafting H3. H3 does not cluster well, so most structures have high dihedral distance and RMSD to the cluster center. Due to this, cluster-based dihedral constraints for H3 are not used. Sequence profiles can be used for clusters, but not usually.
Default: true

-use_only_H3_kinked <Boolean>

Remove any non-kinked CDRs from the CDRSet if grafting H3. For now, the match is based on the ramachandran area of the last two residues of the H3. Kinked in this case is defined as having AB or DB regions at the end. Will be improved for detection.
Default: false

If designing Framework positions, use conservative mutations instead of all of them.
Default: true

-design_H3_stem <Boolean>

Enable design of the first 2 and last 3 residues of the H3 loop if sequence designing H3. These residues play a role in the extended vs kinked H3 conformation. Designing these residues may negatively effect the overall H3 structure by potentially switching a kinked loop to an extended and vice versa. Rosetta may get it right. But it is off by default to err on the cautious side of design. Sequence designing H3 may be already risky.
Default: false

-design_proline <Boolean>

Enable proline design. Profiles for proline are very good, but designing them is a bit risky. Enable this if you are feeling daring.
Default: false

-sample_zero_probs_at <Real>

Value for probabilstic design. Probability that a normally zero prob will be chosen as a potential residue each time packer task is called. Increase to increase variablility of positions.
Default: 0

-force_mutate_framework_for_cluster <Boolean>

Force framework mutations that maintain certain clusters. Currently L1-11-1 vs L1-11-2. See North cluster paper for these dependencies, or checkout rosetta/database/sampling/antibodies/design/cluster_framework_mutations.txt
Default: true

-no_profile_probabilities <Boolean>

Set to sample all available AAs per position instead of sampling based on weights. Used to increase diversity and testing purposes.
Default: false

-seq_design_stats_cutoff <Integer>

Value for probabilistic -> conservative sequence design switch. If number of total sequences used for probabilistic design for a particular cdr cluster being designed is less than this value, conservative design will occur. More data = better predictability.
Default: 10

-seq_design_profile_samples <Integer>

If designing using profiles, this is the number of times the profile is sampled each time packing done. Increase this number to increase variability of designs - especially if not using relax as the mintype.
Default: 1

KT used for the outer graft Monte Carlo. Each graft step will use this value
Default: 1.0

-random_start <Boolean>

Start graft design (currently) with a new set of CDRs from the CDRSets as to not bias the run with native CDRs.
Default: false

-adapt_graft <Boolean>

Adapt the grafting algorithm to increase rate of closed grafts. Takes more time. Grafts that cannot be closed may not be very compatable with the framework in the first place.
Default: true

-enable_adapt_graft_cartesian <Boolean>

Cartesian minimization seems to be causing numerous bugs since the Lukis AST pointer rewrite. These only happen on the cluster and it is very difficult to reproduce them. Until this is fixed, we can skip the cartesian adaptation where cartesian minimization would run when the graft could not close properly. Exceptions are wrapped so that when it does fail we skip the graft. Set this to false to disable its use
Default: false

-remove_antigen <Boolean>

Remove the antigen from the pose before doing any design on it
Default: false

-add_graft_log_to_pdb <Boolean>

Add the full graft log to the output pose. Must also pass -pdb_comments option.
Default: true

Number of c-terminal ~tail~ residues to make flexible (terminus inclusive)
Default: 3

-two_ubiquitins <Boolean>

Mind-blowing - use two ubiquitins (assembled for a K48 linkage) to try to examine the transition state. Don't use this option unless trying to reproduce publication XXXX
Default: false

-extra_bodies <FileVector>

extra structures to add before modeling. Should be in the coordinate frame of the non-moving partner. Will not move during modeling. Will be detected as part of the nonmoving body for repacking purposes.
Default: ""

-UBQ2_lys <Integer>

which Lys on the second UB will be conjugated
Default: 48

-UBQ2_pdb <File>

PDB for second ubiquitin (second moving chain). Only active if -two_ubiquitins is used; inactive otherwise. Optional; defaults to value of -UBQpdb if not passed.

-dont_minimize_omega <Boolean>

disable minimization of omega angles near thioester in MoveMap; not present in original publications (Saha; Baker)
Default: false

-pdz <Boolean>

For the UBQ_Gp_LYX-Cterm executable, if -publication is already on, switch to the PDZ center of mass instead of ubiquitin center of mass for the extra statistics calculations. Don't use this option unless trying to reproduce publication XXXX
Default: false

-GTPasepdb <File>

GTPase structure, or the structure of the thing that is attached to (has cysteine) and does not move; should be one chain
Default: "2OB4.pdb"

-GTPase_residue <Integer>

GTPase lysine (PDB numbering) (where the ubiquitin gets attached; assumed to be on the first chain of GTPase_pdb
Default: 85

Radius list of different level of cluster
Default: utility::vector1<float>(1, 2.0)

-K_n_cluster <IntegerVector>

How many clusters in each level
Default: utility::vector1<int>(1, 10000)

-K_style <StringVector>

Which K-cluster engine to use
Default: utility::vector1<std::string>(9, "GKC")

-K_n_sub <Integer>

Number of clusters in subdir
Default: 100

-K_deque_size <Integer>

Size of subcluster deque
Default: 20

-K_deque_level <Integer>

Provide deque in top level
Default: 1

-K_redundant <Boolean>

Keep all the higher level center structure in sub-pools
Default: true

-K_not_fit_xyz <Boolean>

Do not rotate xyz when calculate rmsd
Default: false

-K_save_headers <Boolean>

Save headers in silent file
Default: false

-score_diff_cut <Real>

score difference cut for RNA and SWA clustering
Default: 1000000.0

-auto_tune <Boolean>

autotune rmsd for clustering between 0.1A up to 2.0A, for SWA clusterer
Default: false

-write_centers <Boolean>

Write out a silent file with the cluster centers
Default: false

cluster:energy_based_clustering

-energy_based_clustering <Boolean>

energy_based_clustering option group

-prerelax <Boolean>

Should imported structures be subjected to a round of fast relaxation? Default false.
Default: false

-relax_rounds <Integer>

The number of fastrelax rounds to apply if the -cluster:energy_based_clustering:prerelax option is used. Default 1.
Default: 1

-cluster_by <String>

What should I use as the basis for clustering? Options are bb_cartesian (xyz coordinates of backbone atoms) and bb_dihedral (phi, psi, omega angles). Default is bb_cartesian.
Default: "bb_cartesian"

-use_CB <Boolean>

If clustering by backbone Cartesian coordinates, should beta carbons be included? Default false. Note that if this option is used, none of the input structures can contain glycine.
Default: false

-cluster_radius <Real>

The radius for clustering, in Angstroms for Cartesian clustering and degrees for dihedral clustering. Default 1.0.
Default: 1.0

-residues_to_ignore <IntegerVector>

List of residues to ignore in alignments for clustering. Default empty list.

-chains_to_ignore <IntegerVector>

List of chains to ignore in alignments for clustering. Default empty list.

-limit_structures_per_cluster <Integer>

Maximum number of structures to output per cluster. Default no limit (0).
Default: 0

-limit_clusters <Integer>

Maximum number of clusters to output. Default no limit (0).
Default: 0

-cyclic <Boolean>

If true, constraints are added to make a peptide bond between the N- and C-termini. If false (default), the termini are free. Default false.
Default: false

-cyclic_symmetry <Integer>

If provided, structures that do not have the desired symmetry are filtered out. Set to 2 for C2 or S2 symmetry, 3 for C3 symmetry, 4 for C4 or S4 symmetry, etc. Unused (0) if not specified. Can only be used with the -cluster:energy_based_clustering:cyclic flag.
Default: 0

-cyclic_symmetry_mirroring <Boolean>

If true, then SN symmetry is used instead of CN. Unused if not specified. Can only be used with the -cluster:energy_based_clustering:cyclic and -cluster:energy_based_clustering:cyclic_symmetry flags.
Default: false

-cyclic_symmetry_threshold <Real>

The angle threshold, in degrees, for determining whether a cyclic peptide is symmetric. Can only be used with the -cluster:energy_based_clustering:cyclic and -cluster:energy_based_clustering:cyclic_symmetry flags. Defaults to 10.0 degrees.
Default: 10.0

-cluster_cyclic_permutations <Boolean>

If true, all cyclic permutations are tried when comparing two structures for clustering. Requires -cluster:energy_based_clustering:cyclic true. Default false.
Default: false

-cyclic_permutation_offset <Integer>

1 by default, meaning that every cyclic permutation is clustered if -cluster:energy_based_clustering:cluster_cyclic_permutations is true. Values X > 1 mean that cyclic permutations shifted by X residues will be clustered.
Default: 1

-perform_ABOXYZ_bin_analysis <Boolean>

If true, Ramachandran bin analysis is performed on all clusters using the A, B, X, Y, and O bins as defined in Hosseinzadeh, Bhardwaj, Mulligan et al. (2018). Inputs must be all-alpha amino acid or peptoid structures. False by default.
Default: false

-mutate_to_ala <Boolean>

If true, the input structures will be converted to a chain of alanines (L- or D-) before scoring. Default false.
Default: false

-disulfide_positions <IntegerVector>

A space-separated list of positions that are disulfide-bonded. For example, -cluster:energy_based_clustering:disulfide_positions 3 8 6 23 would mean that residues 3 and 8 are disulfide-bonded, as are residues 6 and 23. Defaults to an empty list of the option is not specified, in which case disulfides are auto-detected.

-homooligomer_swap <Boolean>

If the structures contain multiple chains with identical sequence, setting this to true will test all permutations of chains when clustering. Default false.
Default: false

-silent_output <Boolean>

Write output to a silent file instead of to separate PDBs. This will create two files: one that only contains the first member of each cluster, and one that contains everything. Default false.
Default: false

-cst_file <FileVector>

An optional, user-specified list of one or more constraints files. Default unused.

-extra_rms_atoms <StringVector>

A list of additional atoms to use in the RMSD calculation, each in the format residue:atomname separated by whitespace. For example, -extra_rms_atoms 7:SG 12:CG 12:CD 12:CE 12:NZ 14:OG. Default empty list.

-rebuild_all_in_dihedral_mode <Boolean>

If true, full poses are rebuilt for output when clustering in dihedral mode. If false, only backbones are written out. True by default.
Default: true

KIC will try to change the torsion angles of a segment this many residues long. The rotamer of the middle residue will be designed, thus kic_loop_size must be an odd number so a middle residue exists. (Backrub segment length is hardcoded in ShortBackrubMover as 3-residue, or 4-residue if it hits a Proline).
Default: 9

-kic_perturber <String>

Which perturber to use during kinematic closure (KIC). Current options are walking (default) or fragment. Walking perturber adjusts torsions by degrees, the magnitude of which can be set by -walking_perturber_magnitude. If you specify walking you MAY also specify -walking_perturber_magnitude. If you specify fragment you MUST also specify -loops::frag_files and -loops::frag_sizes.
Default: "walking"

-backbone_mover <String>

Which backbone mover to use. Current options are backrub (default) or kic. Backrub does not require additional flags, and uses ShortBackrubMover which is hardcoded for 3-residue segments (or 4-residue if it hits a Proline). Kic optionally takes extra flag -kic_perturber.
Default: "backrub"

True = For each packable position, ClashBasedShellSelector iterates through rotamers to determine if the residue could clash with any designable positions. If a clash isnt possible, the packable position is changed from NATAA to NATRO. False = Perform side chain moves strictly as defined in resfile. Default true reproduces behavior from Ollikainen 2015.
Default: true

cp

-cp <Boolean>

cp option group

-cutoff <Real>

designable neighbor cutoff
Default: 16

-relax_sfxn <String>

score function for final relaxation step
Default: "score12_full"

-pack_sfxn <String>

score function for mutational trials
Default: "gauss"

-minimizer_score_fxn <String>

score function for initial minimization
Default: "score12_full"

-output <String>

file where we want to dump the final pose
Default: "final_mutant.pdb"

-ncycles <Integer>

how many cycles to run refinement for
Default: 0

-max_failures <Integer>

how many failures to tolerate at each iteration before quitting
Default: 1

-print_reports <Boolean>

print reports to text file?
Default: false

-vipReportFile <String>

File to print reports to
Default: "reports.txt"

-exclude_file <String>

Optional input file to specify positions that should not be mutated
Default: "cp_excludes"

If true, then the chainbreak energy is used to preserve any N-to-C peptide bond (assuming that this is an N-to-C cyclic peptide). If false, then constraints are used instead. True by default.
Default: true

-rand_checkpoint_file <String>

The name of the checkpoint file used for the random number generator. Defaults to rng.state.gz. Not used if the -cyclic_peptide:checkpoint_job_identifier flag isn't used.
Default: "rng.state.gz"

-checkpoint_file <String>

The name of the checkpoint file. Defaults to checkpoint.txt. Not used if the -cyclic_peptide:checkpoint_job_identifier flag isn't used.
Default: "checkpoint.txt"

-checkpoint_job_identifier <String>

A unique job name for checkpointing. If none is provided, jobs are not checkpointed.
Default: ""

-exclude_residues_from_rms <IntegerVector>

A list of residues that should be excluded from the RMSD calculation. Not used if not provided.

-default_rama_sampling_table <String>

A custom rama table used for sampling, applied by default to all residues unless the –cyclic_peptide:rama_sampling_table_by_res flag overrides this. Default unused (in which case the default rama tables for each residue type are used).
Default: ""

-rama_sampling_table_by_res <StringVector>

Custom rama tables that are to be used for sampling on a per-residue basis. These must be specified as pairs of [residue_index table_name]. For example: -rama_sampling_table_by_res 2 flat_symm_gly_ramatable 3 flat_symm_pro_ramatable. Specified values override the -default_rama_sampling_table at the relevant positions.

-sequence_file <String>

Filename of a file specfying the sequence, as a series of whitespace-separated full residue names (e.g. ALA LYS DARG DPRO HYP). Required input for the simple_cycpep_predict app.

-genkic_closure_attempts <Integer>

How many closure attempts should we make for each job attempted by the simple_cycpep_predict app? Default 1,000.
Default: 1000

-genkic_min_solution_count <Integer>

How many solutions should genKIC find before picking one when used in the simple_cycpep_predict app? Default 1.
Default: 1

-cyclic_permutations <Boolean>

Should cyclic permutations of the sequence be considered when setting up the kinematic closure? Default true.
Default: true

-use_rama_filter <Boolean>

Should GenKIC solutions be filtered based on rama score in the simple_cycpep_predict app? True by default.
Default: true

-rama_cutoff <Real>

The maximum rama score value that's permitted in the accepted GenKIC solutions if the use_rama_filter option is passed to the simple_cycpep_predict app. Default 0.8.
Default: 0.8

-high_hbond_weight_multiplier <Real>

In parts of the simple_cycpep_predict protocol involving upweighting of the backbone hbond terms, by what factor should backbone hbond energy be upweighted? Default 10.0.
Default: 10.0

-min_genkic_hbonds <Real>

The minimum number of backbone hbonds for a solution to pass during GenKIC closure in the simple_cycpep_predict app. Default 3.
Default: 3.0

-min_final_hbonds <Real>

The minimum number of backbone hbonds for a solution to pass after final relaxtion in the simple_cycpep_predict app. Default 0 (report only).
Default: 0.0

-total_energy_cutoff <Real>

An absolute energy threshold, above which solutions are discarded. Unused if not specified.
Default: 0.0

-hbond_energy_cutoff <Real>

The mainchain hbond energy threshold for something to be counted as a hydrogen bond in the simple_cycpep_predict app. Default -0.25.
Default: -0.25

-do_not_count_adjacent_res_hbonds <Boolean>

When counting hydrogen bonds to a residue, should we skip hydrogen bonds to adjacent residues? Default true.
Default: true

-fast_relax_rounds <Integer>

The number of rounds of FastRelax to perform at each FastRelax step in the simple_cycpep_predict protocol. Note that there are two such steps: a high-hbond initial FastRelax applied to all GenKIC solutions, and a regular scorefunction final FastRelax applied to the best GenKIC solution. Default 3.
Default: 3

-count_sc_hbonds <Boolean>

Should sidechain-backbone and sidechain-sidechain hydrogen bonds be counted in the total hydrogen bond count in the simple_cycpep_predict protocol? Default false.
Default: false

-require_disulfides <Boolean>

If true, accepted conformations must permit disulfides to be formed. All permutations of disulfides will be considered, between all disulfide-forming residues. Default false.
Default: false

-disulf_cutoff_prerelax <Real>

If require_disulfides is true, this is the maximum disulfide energy per disulfide bond that is allowed prior to relaxation. If the energy exceeds this value, the solution is rejected. Default 15.0.
Default: 15.0

-disulf_cutoff_postrelax <Real>

If require_disulfides is true, this is the maximum disulfide energy per disulfide bond that is allowed following relaxation. If the energy exceeds this value, the solution is rejected. Default 0.5.
Default: 0.5

-user_set_alpha_dihedrals <RealVector>

Allows the user to specify the dihedrals values at one or more alpha-amino acid positions in the peptide. The flag must be followed by groups of four numbers, where the first is the sequence position and the second, third, and fourth are the phi, psi, and omega values, respectively. Not used if not specified.

-user_set_alpha_dihedral_perturbation <Real>

A small, random perturbation added to all dihedral values set with the -user_set_alpha_dihedrals value. Zero if not specified.
Default: 0.0

-bondlength_perturbation_magnitude <Real>

If used, this is the magnitude (in Angstroms) of the perturbation to apply to mainchain bond lengths when closing with GenKIC. This can be useful for small, strained macrocycles. No bond length perturbation is applied if this option is not specified.
Default: 0.0

-bondangle_perturbation_magnitude <Real>

If used, this is the magnitude (in degrees) of the perturbation to apply to mainchain bond angles when closing with GenKIC. This can be useful for small, strained macrocycles. No bond angle perturbation is applied if this option is not specified.
Default: 0.0

-filter_oversaturated_hbond_acceptors <Boolean>

If true, sampled conformations with more than the allowed number of hydrogen bonds to an acceptor are discarded. True by default.
Default: true

-hbond_acceptor_energy_cutoff <Real>

The hydrogen bond energy above which we do not count a hydrogen bond. Default -0.1.
Default: -0.1

-sample_cis_pro_frequency <Real>

The fraction of the time that omega=0 degrees is sampled at positions preceding L-proline or D-proline. Defaults to 0.3. Set this to 0.0 to prevent all cis-pro sampling.
Default: 0.3

-design_peptide <Boolean>

If true, then design is attempted for every conformation sampled that passes filters. Default false.
Default: false

-allowed_residues_by_position <File>

A text file that lists allowed amino acid resides at each position in the peptide. Each line must be a whiltespace-separated list of full amino acid names, with the positon index at the start of the line. Optionally, a DEFAULT setting may be provided (where DEFAULT replaces the position index), which is applied to all positions in the absence of a line describing what's allowed at that position. In the absence of a DEFAULT line, non-specified positions are repacked with no design. Not used if not specified (in which case all D- and L-amino acids except cysteine, glycine, and methionine are allowed at all positions).

-prohibit_D_at_negative_phi <Boolean>

If design is allowed, should D-amino acid residues be prohibited at positions with negative phi values? Default true.
Default: true

-prohibit_L_at_positive_phi <Boolean>

If design is allowed, should L-amino acid residues be prohibited at positions with positive phi values? Default true.
Default: true

-L_alpha_comp_file <File>

If design is allowed, this is the (optional) aa_composition file used for the right-handed (L-amino acid) alpha-helical region of Ramachandran space. Unused if not specified.

-D_alpha_comp_file <File>

If design is allowed, this is the (optional) aa_composition file used for the left-handed (D-amino acid) alpha-helical region of Ramachandran space. Unused if not specified.

-L_beta_comp_file <File>

If design is allowed, this is the (optional) aa_composition file used for the negative-phi (L-amino acid) beta-strand region of Ramachandran space. Unused if not specified.

-D_beta_comp_file <File>

If design is allowed, this is the (optional) aa_composition file used for the positive-phi (D-amino acid) beta-strand region of Ramachandran space. Unused if not specified.

-angle_relax_rounds <Integer>

The number of rounds of FastRelax to perform with flexible bond angles after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
Default: 0

-angle_length_relax_rounds <Integer>

The number of rounds of FastRelax to perform with flexible bond angles and bond lengths after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
Default: 0

-cartesian_relax_rounds <Integer>

The number of rounds of Cartesian FastRelax to perform after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
Default: 0

-use_classic_rama_for_sampling <Boolean>

If true, classic Ramachandran tables are used for sampling instead of the RamaPrePro tables. Default false (i.e. newer RamaPrePro tables are used by default).
Default: false

-n_methyl_positions <IntegerVector>

If provided, then these positions are N-methylated. Not used if not specified.

-lariat_sidechain_index <Integer>

If a lariat cyclization type is specified (e.g. nterm_isopeptide_lariat, cterm_isopeptide_lariat), then this is the residue that provides the side-chain that connects to the N- or C-terminus of the peptide. If not specified, the residue of appropriate type closest to the other end is used.
Default: 0

-sidechain_isopeptide_indices <IntegerVector>

If the sidechain_isopeptide cyclization type is specified, these are the indices of the residues that are linked by a sidechain-sidechain isopeptide bond to make the loop. If not specified, the residues furthest apart of appropriate types are used. Note that exactly two indices must be given.

-TBMB_positions <IntegerVector>

If provided, then these positions will be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker. 3N positions must be specified, and every group of three will be linked. Unused if not specified.

-use_TBMB_filters <Boolean>

If true, then filters are applied based on distance between TBMB cysteines and on constraints to discard GenKIC solutions that can't be crosslinked easily. True by default.
Default: true

-TBMB_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for TBMB cysteines. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-TBMB_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for TBMB cysteines. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-link_all_cys_with_TBMB <Boolean>

If true, then all cysteine residues in the peptide are linked with 1,3,5-tris(bromomethyl)benzene. There must be exactly three cysteine residues for this flag to be used, and it cannot be used with the -TBMB_positions flag. False/unused by default.
Default: false

-TMA_positions <IntegerVector>

If provided, then these positions will be linked by a trimesic acid crosslinker. The positions must have sidechain primary amines (i.e. be one of lysine [LYS], ornithine [ORN], 2,4-diaminobutyric acid [DAB], or 2,3-diaminopripionic acid [DPP]. There must be 3N positions specified, and every group of three will be linked. Unused if not specified.

-use_TMA_filters <Boolean>

If true, then filters are applied based on distance between TMA-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked easily. True by default.
Default: true

-TMA_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by trimseic acid (TMA). Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-TMA_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by trimseic acid (TMA). Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-square_pyramidal_metal_positions <StringVector>

If provided, then these positions will coordinate a metal with square pyramidal coordination. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,res4,res5,metal. For example, if positions 4, 6, 9, 13, and 16 were to coordinate a nickel, the string would be 4,6,9,13,16,Ni2. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_square_pyramidal_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-square_pyramidal_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a metal coordinated with square pyramidal coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-square_pyramidal_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a metal coordinated with square pyramidal coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-square_planar_metal_positions <StringVector>

If provided, then these positions will coordinate a metal with square planar coordination. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,res4,metal. For example, if positions 6, 9, 13, and 17 were to coordinate a nickel, the string would be 6,9,13,17,Ni2. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_square_planar_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-square_planar_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a metal coordinated with square planar coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-square_planar_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a metal coordinated with square planar coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-trigonal_pyramidal_metal_positions <StringVector>

If provided, then these positions will coordinate a metal with trigonal pyramidal coordination. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,metal. For example, if positions 6, 9, and 13 were to coordinate a zinc, the string would be 6,9,13,Zn. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_trigonal_pyramidal_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-trigonal_pyramidal_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a metal coordinated with trigonal pyramidal coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-trigonal_pyramidal_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a metal coordinated with trigonal pyramidal coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-trigonal_planar_metal_positions <StringVector>

If provided, then these positions will coordinate a metal with trigonal planar coordination. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,metal. For example, if positions 6, 9, and 13 were to coordinate a zinc, the string would be 6,9,13,Zn. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_trigonal_planar_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-trigonal_planar_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a metal coordinated with trigonal planar coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-trigonal_planar_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a metal coordinated with trigonal planar coordination. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-tetrahedral_metal_positions <StringVector>

If provided, then these positions will coordinate a metal, tetrahedrally. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,res4,metal. For example, if positions 4, 6, 9, and 13 were to coordinate a zinc, the string would be 4,6,9,13,Zn. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_tetrahedral_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-tetrahedral_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a tetrahedrally-coordinated metal. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-tetrahedral_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a tetrahedrally-coordinated metal. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-octahedral_metal_positions <StringVector>

If provided, then these positions will coordinate a metal, octahedrally. The positions must have sidechains that can coordinate a metal (e.g. histidine, aspartate, glutamate). The positions should be specified in the form res1,res2,res3,res4,res5,res6,metal. For example, if positions 4, 6, 9, 13, 16, and 18 were to coordinate an iron(II), the string would be 4,6,9,13,Fe2. Multiple sets of metal-coordinating side-chains can be specified, separated by a space. The metal will be represented by virtual atoms, and will not be modelled explicitly. Unused if not specified.

-use_octahedral_metal_filters <Boolean>

If true, then filters are applied based on distance between metal-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked with a metal easily. True by default.
Default: true

-octahedral_metal_sidechain_distance_filter_multiplier <Real>

A multiplier for the distance cutoff for side-chains linked by a octahedrally-coordinated metal. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-octahedral_metal_constraints_energy_filter_multiplier <Real>

A multiplier for the constraints energy for side-chains linked by a octahedrally-coordinated metal. Higher values result in more permissive filtering. Default 1.0.
Default: 1.0

-require_symmetry_repeats <Integer>

If this option is used, then only backbones that are cN (or cN/m, if mirror symmetry is required) symmetric will be accepted. For example, if set to 2, then only c2-symmetric backbones will be accepted. Unused if not specified.
Default: 1

-require_symmetry_mirroring <Boolean>

If this option is used, then only backbones with mirror symmetry are accepted. Must be used with the -cyclic_peptide:require_symmetry_repeats flag.
Default: false

-require_symmetry_angle_threshold <Real>

The cutoff, in degrees, to use when comparing mainchain torsion values to determine whether symmetry repeats are truely symmetric. Defaults to 10 degrees.
Default: 10.0

-require_symmetry_perturbation <Real>

If provided, this is the magnitude of the perturbation to apply when copying mainchain dihedrals for symmetric sampling. Allows slightly asymmetric conformations to be sampled. Default is 0.0 (no perturbation).
Default: 0.0

-MPI_auto_2level_distribution <Boolean>

If true, will automatically set up job distribution with one emperor talking to N-1 slaves, where N is the total number of processes. Cannot be used with -MPI_processes_by_level. Default false.
Default: false

-MPI_processes_by_level <IntegerVector>

The number of processes at each level of the parallel communications hierarchy, used only by the MPI version. For example, '1 10 100' would mean that one emperor would talk to 10 masters, which would talk to 100 slaves (implying that each master is assigned 10 slaves). Similarly, '1 100' would mean that one master would talk directly to 100 slaves. Required for the MPI version.

-MPI_batchsize_by_level <IntegerVector>

The number of jobs sent at a time by each communication level to its children. Given N levels, N-1 values must be specified. For example, given 3 communications levels, '100 10' would mean that the emperor sends 100 jobs at a time to each master, which sends 10 jobs at a time to each slave. Must be specified for the helical_bundle_predict and simple_cycpep_predict applications in MPI mode.

-MPI_sort_by <String>

The MPI versions of the helical_bundle_predict and simple_cycpep_predict applictions have the option of writing out the top N% of solutions. This determines the sort metric.
Default: "energy"

-MPI_choose_highest <Boolean>

When outputing the top N% of solutions, should I choose the ones with the highest score for the metric chosen (energy, rmsd, hbonds, etc.) or lowest? Default false (chose lowest).
Default: false

-MPI_output_fraction <Real>

The fraction of total structures that will be written out. This is used in conjunction with 'MPI_sort_by' to output the top N% of job outputs. For example, '-MPI_output_fraction 0.05 -MPI_sort_by rmsd' means that the 5% of structures with the lowest RMSD values will be written out.
Default: 1.0

-MPI_stop_after_time <Integer>

If this option is used, the emperor node will send a stop signal after an elapsed period of time, given in seconds. Slave jobs currently running will continue, but intermediate masters will not assign any more work. Useful on HPC clusters with time limits, to ensure that jobs completed are collected at the end. Unused if not specified.

-MPI_pnear_lambda <Real>

In MPI mode a goodness-of-funnel metric is automatically calculated at the end (PNear). This value may be thought of as the probability, from 0 to 1, of the peptide being in the native conformation at any given time. The parameter lambda controls the breadth of the Gaussian (in RMSD units – Angstroms) that is used to determine the extent to which a state is native-like. Default 0.5 A.
Default: 0.5

-MPI_pnear_kbt <Real>

In MPI mode a goodness-of-funnel metric is automatically calculated at the end (PNear). This value may be thought of as the probability, from 0 to 1, of the peptide being in the native conformation at any given time. The parameter kbt is the Boltzmann temperature that determines the extent to which higher energy states are likely to be sampled. Default 1.0 kcal/mol.
Default: 1.0

-threads_per_slave <Integer>

In the multi-threaded MPI compilation, this is the number of threads to launch per slave process. Note that emperor and master-layer processes do not launch threads. A value of 1 (the default) means that only standard hierarchical process-based parallelism will be used. In non-MPI or non-threaded compilations, this option is unused.
Default: 1

-compute_rmsd_to_lowest <Boolean>

If true the RMSD to the top structure (by whatever ranking) is computed in addition to the RMSD to a user-supplied native (if a native structure is provided). False by default. Only used in MPI version of Rosetta.
Default: false

-compute_ensemble_sasa_metrics <Boolean>

If true, the Boltzmann-weighted SASA, polar SASA, hydrophobic SASA, and number of unsatisfied polar groups is computed (ensemble average). False by default. Only used in MPI version of Rosetta.
Default: false

list of one or more positions in the input pdb, eg: -pdb_pos 125:A 127:A 4:C
Default: ""

-methylate <StringVector>

list of one or more positions in the input pdb to be methylated, eg: -methylate 125:A 127:A 4:C
Default: ""

-dna_backbone_torsion_sdevs <RealVector>

No description

-dna_sugar_torsion_sdev <Real>

No description
Default: 4.0

-dna_chi_torsion_sdev <Real>

No description
Default: 15.0

-lk_ball_wtd_tag <String>

No description

-lk_ball_for_bb <Boolean>

No description
Default: true

-lk_ball_ramp_width_A2 <Real>

No description
Default: 3.9

-lk_ball_overlap_gap <Real>

No description
Default: 0.0

-lk_ball_overlap_width_A2 <Real>

No description
Default: 5.0

-lk_ball_water_fade <Real>

No description
Default: 1.0

-lk_ball_wtd_prefactors <RealVector>

6 scale factors that are applied to the lk_ball_wtd per-atom weights; the order is <donor-iso> <donor-ball> <acceptor-iso> <acceptor-ball> <don+acc-iso> <don+acc-ball>; where <don+acc> means atom-types that are both donors and acceptors (SP3 hybridized OH for example)

-lk_ball_waters_sp2 <RealVector>

The geometry of sp2 acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 120 0 2.65 120 180. No limit on #, but all three params must be specified for each

-lk_ball_waters_sp3 <RealVector>

The geometry of sp3 acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 109 120 2.65 109 240. No limit on #, but all three params must be specified for each

-lk_ball_waters_ring <RealVector>

The geometry of ring acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 180 0. No limit on #, but all three params must be specified for each

Prefix to use when dumping trajectories with dump_trajectory ScoreType.
Default: "traj"

-gz <Boolean>

Dump trajectories in .pdb.gz format.
Default: false

-stride <Integer>

The stride for trajectory dumping. This defaults to 1, meaning that a pose is dumped for every function call. Higher values dump a pose after every Nth function call, allowing sparser sampling of trajectories.
Default: 1

allows backbone of active site residues to move during cst_opt and cst_min. In the cst_opt stage, residue Cas will be constrained to their original positions.
Default: false

-bb_min_allowed_dev <Real>

distance by which Cas are allowed to move during backbone minimization before a penalty is assigned.
Default: 0.5

-loop_bb_min_allowed_dev <Real>

distance by which Cas are allowed to move during backbone minimization before a penalty is assigned. Applied only for loops as determined by DSSP.
Default: 0.5

-minimize_ligand_torsions <Real>

degrees by which ligand torsions are allowed to rotate before a penalty is assigned. Only those torsions which have diversity in the conformational ensemble are allowed this std dev. rest are constrained to 0.1
Default: 10.0

yes/no? Create loop pdb files named loopreg_[regionid]_[whichsample].pdb for the chosen loop samples; if 'quit_afterwards' is given, then the program exits after all loops have been generated
Default: "no"

-fix_catalytic_aa <Boolean>

preventing catalytic aa from repacking
Default: false

-additional_packing_ligand_rb_confs <Integer>

Ligand Rotamers will be built at additional random rigid body positions during packing
Default: 0

-ex_catalytic_rot <Integer>

convenience option to use higher number of rotamers for catalytic residues. The chosen level will be applied to all chis of every catalytic residue.
Default: 1

-single_loop_ensemble_size <Integer>

number of conformations generated for each of the independent loops in a flexbb calculation
Default: 100

-loop_generator_trials <Integer>

number of trials of that the respective loop generator(backrub/kinematic kic) does in enzdes flexbb
Default: 200

Fragment uniqueness filter. On by default. Minimum CA/CB average deviation that at least one residue must have from all other already-included fragments for a new fragment to be included
Default: 0.3

-max_bb_deviation <Real>

Fragment smoothness filter. Off by default. Upper limit on the backbone average deviation a new fragment may have to its most-similar fragment that has already been included in the fragment set.
Default: 0.1

-max_bb_deviation_from_startstruct <Real>

Fragment native-proximity Filter. Always on. Maximum tolerated backbone average deviation from the starting backbone for a fragment that to be included in the fragment set.
Default: 1.5

-remodel_trials <Integer>

how often each loop is being remodeled in the enzdes_remodel mover
Default: 100

-remodel_secmatch <Boolean>

if constrained interactions are missing in the pose during remodel, the SecondaryMatcher will be used to try to find them in the remodeled region. very experimental at this point
Default: false

-dump_inverse_rotamers <Boolean>

in case of remodel secmatching against inverse rotamers, these rotamers will be dumped before the protocol starts for visual inspection by the user
Default: false

-remodel_aggressiveness <Real>

determines the aggressiveness with which a given loop is remodeled. legal values between 0 and 1, where 1 is aggressive and 0 conservative.
Default: 0.1

-favor_native_res <Real>

a bonus energy assigned to the native res during a design calculation
Default: 0.5

the maximum constraint energy at which a residue is accepted in the secondary matcher
Default: 1.0

-change_lig <File>

Can be used with the secondary matching protocol if different incarnations of the ligand are used for design and primary matching. The file needs to contain information on what atoms to superimpose.
Default: "ligchange_file.txt"

-process_ligrot_separately <String>

In the EnzdesFixBB protocol, causes the protocol to be executed separately for all non_bb clashing ligand rotamers.
Default: "default_lig"

-start_from_random_rb_conf <Boolean>

In the EnzdesFixBB protocol, if there are additional ligand rigid body conformations available (from a multimodel pdb), a random one of these will be the starting point for the protocol.
Default: false

-bb_bump_cutoff <Real>

option to specify the maximum allowed backbone energie when replacing a new residue type
Default: 2.0

-sc_sc_bump_cutoff <Real>

option to specify the maximum allowed energy between two newly placed sidechains in the secondary matcher
Default: 2.0

-no_packstat_calculation <Boolean>

will determine whether the computationally intensive packstat calculation will be done at the end of a run
Default: false

-compare_native <String>

triggers comparison of every designed structure to its respective native pdb. the value of the option needs to be a directory path that contains all the native pdb files
Default: "./"

-final_repack_without_ligand <Boolean>

if a scorefile is requested, this option triggers every structure to be repacked without the ligand. the resulting structure will be output in a multimodel pdb, and differences in energy and rmsd are added to the scorefile.
Default: false

-dump_final_repack_without_ligand_pdb <Boolean>

If option -final_repack_without_ligand is active, this option will cause the repacked structure to be separately dumped.
Default: false

number of fragment candidates per position; the final fragments will be selected from them
Default: 200

-write_rama_tables <Boolean>

Fragment picker will spit out sequence specific ramachandran score tables for your viewing pleasure. These ramachandran tables are based on the secondary structure predictions fed into RamaScore, and you may occasionally want to look at what the program has defined.
Default: false

-rama_C <Real>

Constant in RamaScore equation, command line is for optimization tests
Default: 0.0

-rama_B <Real>

Constant in RamaScore equation, command line is for optimization tests
Default: 1.0

-sigmoid_cs_A <Real>

Constant in CSScore equation, command line is for optimization tests
Default: 2.0

-sigmoid_cs_B <Real>

Constant in CSScore equation, command line is for optimization tests
Default: 4.0

Filename of a file specfying the sequence, as a series of whitespace-separated full residue names (e.g. ALA LYS DARG DPRO HYP). Required input for the simple_cycpep_predict app unless -in:file:fasta is provided.

-helix_assignment_file <File>

A file containing information about the helix types and helical regions within a helical bundle.
Default: ""

-num_simulated_annealing_rounds_centroid <Integer>

Number of rounds of simulated annealing in centroid mode.
Default: 3

-num_steps_per_simulated_annealing_round_centroid <Integer>

Number of steps in each round of simulated annealing in centroid mode.
Default: 1000

If true, the initial centroid model is converted to a full-atom model and relaxed with the FastRelax protocol. Other refinement steps, such as finding disulfides, may also be carried out. True by default.
Default: true

-fast_relax_rounds <Integer>

The number of rounds of FastRelax that will be applied. Does nothing if do_final_fullatom_refinement is false. Set to 3 by default.
Default: 3

-find_disulfides <Boolean>

If true, the full-atom refinement steps include trying disulfide permutations. Does nothing if do_final_fullatom_refinement is false. True by default.
Default: true

-ignore_native_residues_in_rmsd <IntegerVector>

A whitespace-separated list of residues in the pose provided with -in:file:native which should NOT be used in calculating the RMSD. The alignment will skip these residues. For example, if the generated structures are 10 residues long, the native is 11, and residue 5 is skipped, then residues 1-4 will be aligned to residues 1-4 of the generated structures, and residues 6-11 of the native wil be aligned to resiudues 5-10 of the generated stuctures.

-ignore_prediction_residues_in_rmsd <IntegerVector>

A whitespace-separated list of residues in the generated poses that will be ignored when aligning to the pose provided with -in:file:native. These residues are skipped in the alignment – so if, for example, residues 3 and 4 are specified, and the generated structures are 12 residues long and the native structure is 10 residues long, residues 1-2 of both structures will be aligned, and residues 5-12 of the generaetd structures will be aligned to residues 3-10 of the native.

Residue to use for angle calculation from stubCA, <this option>="">, and stubCB. Used to determine if stub is pointing towards target. 0 uses the default, which is the targets center of mass
Default: 0

-batch_size <Integer>

Run stub hashing in batches of this size. (Ignored if target_res is set)
Default: 10

If true, each side-chain rotamer is minimized using the Rosetta molecular mechanics forcefield prior to scoring. True by default.
Default: true

-mainchain_potential_points_per_dimension <IntegerVector>

The number of points for each dimension in the multidimensional mainchain potential, provided as a whitespace-separated list of integers. Each integer must be strictly positive. Required input.

-mainchain_torsions_covered <IntegerVector>

The mainchain torsions that are covered by this potential. For example, an oligourea has four mainchain torsions, but only torsions 1, 2, and 3 are covered (and the fourth is restrained by the omega scoreterm), in which case this option can be set to 1 2 3. If not specified, it defaults to all mainchain torsions.

-make_pre_proline_potential <Boolean>

If true, then this application will make a potential for a position preceding a proline, sarcosine, peptoid, or other N-substituted building-block. If false (the default), then it generates a potential for a position preceding an unsubstituted position (e.g. the 19 canonical amino acids other than proline).
Default: false

-output_filename <File>

Output file to which the generated mainchain potential will be written. Defaults to generated_mainchain_potential.txt
Default: "generated_mainchain_potential.txt"

-residue_name <String>

The name of the residue type for which we will be generating a mainchain potential. Defaults to ALA if not set, but should be set by the user.
Default: "ALA"

-symmetrize_output <Boolean>

If true, the output will be made symmetric. False by default. Note that this necessitates a five degree offset.
Default: false

-write_potentials_for_individual_scoreterms <Boolean>

If true, a separate potential file is written for each scoreterm. This is used to fit the weights for the molecular mechanics forcefield used by the make_mainchain_potential application. Note that these tables will be written unnormalized and with weights of 1.0 for each term. False by default.
Default: false

match

-match <Boolean>

match option group

-lig_name <String>

Name of the ligand to be matched. This should be the same as the NAME field of the ligand's parameter file (the .params file)

-bump_tolerance <Real>

The permitted level of spherical overlap betweeen any two atoms. Used to detect collisions between the upstream atoms and the background, the upstream atoms and the downstream atoms, and the downstream atoms and the background
Default: 0.0

-active_site_definition_by_residue <File>

File describing the active site of the scaffold as a set of resid/radius pairs

-active_site_definition_by_gridlig <File>

File containing 1s and Os describing the volume of space for the active site. .gridlig file format from Rosetta++

-required_active_site_atom_names <File>

File listing the downstream-residue-atom names which must reside in the defined active site. Requires either the flag active_site_definition_by_residue or the flag active_site_definition_by_gridlig to be specified.

-grid_boundary <File>

File describing the volume in space in which the third orientation atom must lie
Default: ""

-geometric_constraint_file <File>

File describing the geometry of the downstream object relative to the upstream object

-scaffold_active_site_residues <File>

File with the residue indices on the scaffold that should be considered as potential launch points for the scaffold's active site. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
Default: ""

-scaffold_active_site_residues_for_geomcsts <File>

File which lists the residue indices on the scaffold to consider as potential launch points for the scaffold's active site for each geometric constraint; each constraint may have a separate set of residue ids. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
Default: ""

-euclid_bin_size <Real>

The bin width for the 3-dimensional coordinate hasher, in Angstroms
Default: 1.0

-euler_bin_size <Real>

The bin width for the euler angle hasher, in degrees
Default: 10.0

-consolidate_matches <Boolean>

Instead of outputting all matches, group matches and then write only the top -match::output_matches_per_group from each group.
Default: false

-output_matches_per_group <Integer>

The number of matches to output per group. Requires the -match::consolidate_matches flag is active.
Default: 10

-orientation_atoms <StringVector>

The three atoms, by name, on the downstream partner to use to describe its 6 dimensional coordinate; its position and orientation. Only usable when the downstream partner is a single residue. Exactly 3 atom names must be given. If these atoms are unspecified, the matcher will use the residues neighbor atom and two atoms bonded to the neighbor atom to define the orientation. The euclidean coordinate of the third orientation atom is used as the first the dimensions of the downstream residues 6D coordinate; the other three dimensions are the three euler angles described by creating a coordinate frame at orientation atom 3, with the z axis along the vector from orientation atom 2 to orientation atom 3, and the y axis lying in the plane with orientation atoms 1,2&3.

-output_format <String>

The format in which the matches are output
Default: "CloudPDB"

-match_grouper <String>

The parameters that matches are grouped according to by the MatchConsolidator or the CloudPDBWriter
Default: "SameSequenceAndDSPositionGrouper"

-grouper_downstream_rmsd <Real>

Maximum allowed rmsd between two orientations of the downstream pose to be considered part of the same group
Default: 1.5

-output_matchres_only <Boolean>

Whether to output the matched residues only or the whole pose for every match
Default: false

-geom_csts_downstream_output <IntegerVector>

For which of the geometric constraints the downstream residue/ligand will be output
Default: ['1']

-filter_colliding_upstream_residues <Boolean>

Filter the output matches if the hits induce a collision between the upstream residues
Default: true

-upstream_residue_collision_tolerance <Real>

The amount of atom overlap allowed between upstream residues in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
Default: 0.0

-upstream_residue_collision_score_cutoff <Real>

The score cutoff for upstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
Default: 10.0

-upstream_residue_collision_Wfa_atr <Real>

The fa_atr weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
Default: 0.8

-upstream_residue_collision_Wfa_rep <Real>

The fa_rep weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
Default: 0.44

-upstream_residue_collision_Wfa_sol <Real>

The fa_sol weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
Default: 0.0

-filter_upstream_downstream_collisions <Boolean>

Filter the output matches if the hits induce a collision between the upstream residues and the downstream pose
Default: true

-updown_collision_tolerance <Real>

The amount of atom overlap allowed between upstream and downstream atoms in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
Default: 0.0

-updown_residue_collision_score_cutoff <Real>

The score cutoff for upstream/downstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
Default: 10.0

-updown_residue_collision_Wfa_atr <Real>

The fa_atr weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
Default: 0.8

-updown_residue_collision_Wfa_rep <Real>

The fa_rep weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
Default: 0.44

-updown_residue_collision_Wfa_sol <Real>

The fa_sol weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
Default: 0.0

-define_match_by_single_downstream_positioning <Boolean>

Enumerate combinations of matches where a single positioning of the downstream partner as well as the conformations of the upstream residues defines the match; it is significantly faster to enumerate unique matches when they are defined this way instead of enumerating the (combinatorially many) matches when a match is defined by n-geometric-constraint locations of the downstream partner. This faster technique for outputting matches is automatically chosen when the flag -match::output_format is PDB.

-ligand_rotamer_index <Integer>

Match with a particular conformation of the ligand; the index represents which conformation in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. The index of the first conformation in that file is 1; valid indices range from 1 to the number of entries in the multi-model .pdb file. If this command-line flag is not used, then the conformation of the ligand described by the ICOOR_INTERNAL lines of the ligand's .params file is used instead.

-enumerate_ligand_rotamers <Boolean>

Match with all ligand rotamers specified in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. This flag may not be used in combination with the match::ligand_rotamer_index flag. Geometry of the ligand rotamers in the .pdb file will be idealized to the .params file bond angles and lengths.
Default: true

-only_enumerate_non_match_redundant_ligand_rotamers <Boolean>

Only defined if enumerate_ligand_rotamers is true this option causes the matcher to determine which rotamers in the ligand rotamer library are redundant in terms of matching, meaning the atoms they're matched through are superimposable. after having subdivided the ligand rotamer library into match-redundant subgroups, the matcher will then only place the first nonclashing rotamer from each subgroup.
Default: true

-dynamic_grid_refinement <Boolean>

When too many hits land in the same 'connected component', requiring the enumeration of twoo many matches, refine the grid size to be smaller so that fewer matches have to be enumerated. This process works on individual connected components and is not applied to all regions of 6D. This is significantly more efficient than enumerating all matches, while allowing the grid size to remain large and the rotamer and external geometry to remain dense. (A connected component refers to

-build_round1_hits_twice <Boolean>

Memory saving strategy that avoids paying for the storage of all the round-1 hits and instead records only what 6D voxels those hits fall in to. Then the second round of matching proceeds storing only the hits that fall into the same voxels that the hits from the first round fell into. Then the matcher goes back and generates the first-round hits again, but only keeps the ones that land into the same voxels that hits from round 2 fell into. To be used, round 2 must also use the classic match algorithm (and must not use secondary matching).
Default: false

used to dna_motif_collector - controls whether motifs are moved away from original PDB location (comparison is easier if they are moved, so that's default)
Default: false

-pack_score_cutoff <Real>

used in dna_motif_collector - fa_atr + fa_rep energy threshold for a two-residue interaction to determine if it is a motif
Default: -0.5

-hb_score_cutoff <Real>

used in dna_motif_collector - hbond_sc energy threshold for a two-residue interaction to determine if it is a motif
Default: -0.3

-water_score_cutoff <Real>

used in dna_motif_collector - h2o_hbond energy threshold for a two-residue interaction to determine if it is a motif
Default: -0.3

-pack_min_threshold <Real>

Used for motif extraction - packing scores below this value will cause a motif to be discarded
Default: -9999.0

-pack_max_threshold <Real>

Used for motif extraction - packing scores above this value will cause a motif to be discarded
Default: 9999.0

-hbond_min_threshold <Real>

Used for motif extraction - hbond scores below this value will cause a motif to be discarded
Default: -9999.0

-hbond_max_threshold <Real>

Used for motif extraction - hbond scores above this value will cause a motif to be discarded
Default: 9999.0

-elec_min_threshold <Real>

Used for motif extraction - fa_elec scores below this value will cause a motif to be discarded
Default: -9999.0

-elec_max_threshold <Real>

Used for motif extraction - fa_elec scores above this value will cause a motif to be discarded
Default: 9999.0

-duplicate_dist_cutoff <Real>

Value for determining whether a motif is different from others already in a library
Default: 1.0

-duplicate_angle_cutoff <Real>

Value for determining whether a motif is different from others already in a library
Default: 0.4

-motif_output_directory <String>

used in dna_motif_collector - path for the directory where all the collected motifs are dumped as 2-residue pdbs

-eliminate_weak_motifs <Boolean>

used to dna_motif_collector - controls whether only the top 1-2 motifs are counted for every protein position in a protein-DNA interface
Default: true

-duplicate_motif_cutoff <Real>

used in dna_motif_collector - RMSD cutoff for an identical base placed via a motif to see if that motif already exists in a motif library
Default: 0.2

-preminimize_motif_pdbs <Boolean>

used to dna_motif_collector - controls whether the input PDB structure sidechains and bb are minimized before motifs are collected
Default: false

-preminimize_motif_pdbs_sconly <Boolean>

used to dna_motif_collector - controls whether the input PDB structure sidechains are minimized before motifs are collected
Default: false

-place_adduct_waters <Boolean>

used to dna_motif_collector - whether or not adduct waters are placed before motifs are collected, there will be no water interaction calculated if this is false
Default: true

-list_motifs <FileVector>

File(s) containing list(s) of PDB files to process

-motif_filename <String>

File containing motifs

-file_prefix <String>

File containing motifs
Default: "motif"

-build_residue_file <String>

File containing the target positions for building and incorporating motifs

-motif_flexible_loop_file <String>

File containing the flexible loop definition

-residue_trim_file <String>

File a list of residues to trim to Ala before motif incorporation.

-BPData <String>

File containing BuildPosition specific motifs and/or rotamers

-list_dnaconformers <FileVector>

File(s) containing list(s) of PDB files to process

-target_dna_defs <StringVector>

Default: ""

-motif_build_defs <StringVector>

Default: ""

-motif_build_positions <IntegerVector>

-r1 <Real>

RMSD cutoff between motif anchor position and motif target position for allowing a particular motif rotamer to continue on to expand with DNA conformers
Range: 0-
Default: 4.5

-r2 <Real>

RMSD cutoff between motif anchor position and motif target position for accepting the motif
Range: 0-
Default: 1.1

-z1 <Real>

DNA motif specific: cutoff between motif target DNA position and standardized base for allowing a particular motif to continue on to expand with DNA conformers
Range: 0-
Default: 0.75

-z2 <Real>

DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
Range: 0-
Default: 0.95

-dtest <Real>

DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
Range: 0-
Default: 5.5

-rotlevel <Integer>

level of rotamer sampling for motif search
Range: 1-
Default: 5

-num_repacks <Integer>

number of cycles of dropping special_rot weight and design
Range: 0-
Default: 5

-minimize <Boolean>

whether or not to minimize the motifs toward the xtal structure DNA
Default: true

-minimize_dna <Boolean>

whether or not to minimize DNA after every round of design with special_rot weight dropping
Default: true

-run_motifs <Boolean>

whether or not to use motifs in DnaPackerMotif
Default: true

-expand_motifs <Boolean>

whether or not to use expand (use all types) motifs in DnaPackerMotif
Default: true

-aromatic_motifs <Boolean>

whether or not to use expand (use aromatic only types) motifs in DnaPackerMotif
Default: true

-dump_motifs <Boolean>

whether or not to output pdbs with the best rotamer/conformer for each motifs
Default: true

-quick_and_dirty <Boolean>

quick motif run to get a list of all possible motifs before doing a real run
Default: true

-special_rotweight <Real>

starting weight for the weight on motif rotamers
Default: -40.0

-output_file <String>

name of output file for all the best motifs and rotamers or for the dna_motif_collector it is the file where all the motifs are dumped

-data_file <String>

name of output file for any data about how many rotamers and motifs pass what tests, etc

-target_aa <String>

three letter code for the target amino acid for finding motifs
Default: "LEU"

-flex_sugar <Boolean>

whether or not to add the flexible sugar, not using PB way of adding options
Default: true

-clear_bprots <Boolean>

whether or not to clear the rotamers that were read in from a previous run and restart with only the motifs that were read in and the specified rotlevel
Default: true

-rots2add <Integer>

number of rotamers to add to design from the MotifSearch for each amino acid type
Range: 1-
Default: 100

-restrict_to_wt <Boolean>

restrict the motif search to finding motifs of the same amino acid as the starting pose, for homology modeling
Default: true

-rerun_motifsearch <Boolean>

setting the MotifSearch to run again, using the rotamers in the build position, most likely to change stringency or amino acid type on a second run
Default: true

-no_rotamer_bump <Boolean>

skip the bump check when making the rotamers that will be tested for motif interactions, makes code much slower, but it is advised to increase the max_rotbump_energy to at least 10.0 instead of the default of 5.0 if bump_check is being used
Default: false

nmr

nmr:pcs

Number of repeats in non-linear least squares fitting of the PCS tensor.
Range: 1-100
Default: 5

-optimize_tensor <Boolean>

Optimize the lanthanide ion position and other parameters of the PCS tensor after grid search.
Default: false

-multiset_weights <RealVector>

Vector of weights of PCSMultiSets. One PCSMultiSet refers to data collected for multiple lanthanides at one tagging site.

-normalize_data <Boolean>

Normalize PCS data of every experiment by their standard deviation.
Default: false

-use_symmetry_calc <Boolean>

Consider the contribution from symmetric subunits for PCS calculation. Only the PCSs of the asymmetric subunit must to be provided as input. The symmetric residues are deduced from the symmetry information carried by the pose. Alternatively, one can provide all residues contributing to one PCS as an ambiguous atom selection in the input file.
Default: false

-show_info <Boolean>

Show additional information about PCS calculation (experimental vs. back-calculated PCSs and PCS tensor summary) at the end of every ab-initio folding stage.
Default: false

nmr:rdc

-rdc <Boolean>

rdc option group

-input_file <File>

RDC input file.

-nls_repeats <Integer>

Number of repeats in non-linear least squares fitting of the alignment tensor.
Range: 1-100
Default: 5

-multiset_weights <RealVector>

Vector of weights of RDCMultiSets. One RDCMultiSet refers data collected for multiple experiments in one alignment medium.

-use_symmetry_calc <Boolean>

Consider the contribution from symmetric subunits for RDC calculation. Only RDCs of the asymmetric subunit must be provided as input. The symmetric residues are deduced from the symmetry information carried by the pose. This option is still experimental and works so far for cases with C-symmetry and D2-symmetry for which the alignment tensor axes coincide with the symmetry axes.
Default: false

-show_info <Boolean>

Show additional information about RDC calculation (experimental vs. back-calculated RDCs and alignment tensor summary) at the end of every ab-initio folding stage.
Default: false

-normalization_type <String>

Apply scaling of input RDC values. Possible options are NH, CH or none. By default RDCs are expected not to be normalized and will be scaled relative to N-H (i.e. option NH). In case of option CH RDCs will be scaled relative to CA-HA. If option none is chosen it is assumed that RDC values have been normalized to H-N before and thus no additional scaling will be applied.
Default: "NH"

-correct_sign <Boolean>

Use the correct sign of the 15N gyromagnetic ratio and thus of the dipolar coupling constants i.e. positive for NC and NH and negative for CH. Use this option if input couplings have different signs. By default the 15N gyromagnetic ratio is taken to be positive and the dipolar coupling constants to have the same sign.
Default: false

Optimize the position of the paramagnetic ion. Only in combination with a gridsearch.
Default: false

-multiset_weights <RealVector>

Vector of weights of PREMultiSets. One PREMultiSet refers to multiple datasets collected for the same spinlabel site.

-normalize_data <Boolean>

Normalize PRE data of every experiment by their standard deviation.
Default: false

-use_symmetry_calc <Boolean>

Consider the contribution from symmetric subunits for PRE calculation. Only the PREs of the asymmetric subunit must be provided as input. The symmetric residues are deduced from the symmetry information carried by the pose. Alternatively, one can provide all residues contributing to one PRE as an ambiguous atom selection in the input file.
Default: false

-show_info <Boolean>

Show additional information about PRE calculation (experimental vs. back-calculated PREs and PRE spinlabel summary) at the end of every ab-initio folding stage.
Default: false

nmr:spinlabel

-spinlabel <Boolean>

spinlabel option group

-max_ensemble_size <Integer>

Maximum number of spinlabel rotamers that make up the ensemble. If the ensemble size is higher, rotamers are binned to speed up the calculation.
Default: 20

-highres_conformer_filter_type <String>

Type of filtering spinlabel conformers in Rosetta full-atom mode. Possible modes are: DISTANCE and BUMP_ENERGY. Default is BUMP_ENERGY in which case conformers are checked for clashes by their packer energy. The DISTANCE filter detects clashes by measuring the distance of spin-label side-chain heavy atoms to the NBR_ATOM of neighborhood residues.
Default: "BUMP_ENERGY"

-elaborate_rotamer_clash_check <Boolean>

If true, perform an elaborate clash check of every heavy atom of all spinlabel rotamers with the atoms in the surrounding amino acid residues. If all rotamers produce at least one clash, return that rotamer with the lowest number of clashes. If false, consider only heavy atoms in non-clashing rotamers and return a random member in case their are no non-clashing rotamers.
Default: false

nonlocal

Decsribes how the structure is partitioned into chunks. Each residue must be present in 1 and only 1 chunk. Loop file format.

-randomize_missing <Boolean>

Randomize the coordinates of missing loops. This occurs often in broken-chain folding from a sequence alignment and template pdb. Default value is false to preserve existing behavior in ThreadingJobInputter
Default: false

load from silent instead of pdb - uses path of requested pdb to find silent file, each PDB needs to have all of its structures in its own folder (ie: 1agy/pdb_set.silent) - only works in optimize_decoy_discrimination
Default: "pdb_set.silent"

a conventional weightfile that optE will use to determine which weights will be counted. All non-zero weights in the file will contribute to rotamer energies and be fit; use the -optE::fix option to fix any of these weights. Weight values will also be used as starting values for optimization.

-fix <StringVector>

weights to be fixed (must also appear in the weightfile given by the -optE::weights option)

-free <File>

IterativeOptEDriver flag: specify a file to read score types that are free – optionally include a starting weight for each score type

-fixed <File>

IterativeOptEDriver flag: specify a file to read score types and weights for score types that are on but fixed

Do not optimize the weights in the context of the native structure, but rather, start by designing the protein with the input weight set. Requires that all score types listed in -optEfree have specificed weights.

-n_design_cycles <Integer>

The number of outer-loop design cycles to complete; default of 10 after which convergence has usually occurred
Default: 10

With the iterative optE driver, weight the individual components according to the input file – default weight of 1 for all components. Weight file consists of component-name/weight pairs on separate lines: e.g. prob_native_structure 100.0

-optimize_nat_aa <Boolean>

With the iterative optE driver, optimize weights to maximize the probability of the native rotamer

-optimize_nat_rot <Boolean>

With the iterative optE driver, optimize weights to maximize the probability of the native rotamer in the native context

-optimize_ligand_rot <File>

With the iterative optE driver, optimize weights to maximize the probability of the native rotamer around the ligand

-optimize_pssm <Boolean>

With the iterative optE driver, optimize weights to maximize the match between a BLAST generated pssm probabillity distribution

With the iterative optE driver, predict the the ddGmut to be the difference between the straight mean (1/n Sum(E_i)) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.

-optimize_ddGmutation_boltzman_average <Boolean>

With the iterative optE driver, predict the the ddGmut to be the difference between the boltzman average energies ( Sum( E_i * e**-E_i/kT)/Sum( e**-E_i/kT) ) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.

-exclude_badrep_ddGs <Real>

With the iterative optE driver, consider only ddG data where the unweighted repulsive energy delta mut-wt < given value

-pretend_no_ddG_repulsion <Boolean>

With the iterative optE driver, set all repulsive scores to zero when looking for ddG correlations

-optimize_decoy_discrimination <File>

With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.

-normalize_decoy_score_spread <String>

In decoy discrimination optimization, normalize both the native and decoy energies generated by a set of weights by sigma_curr /sigma_start where sigma_start is computed as the standard deviation of the decoy energies given an input weight set

-ramp_nativeness <Boolean>

In decoy discrimination optimization, give structures in the range between max_rms_from_native and min_decoy_rms_to_native a nativeness score (which ramps linearly from 1 to 0 in that range) and include scores from structures in the numerator of the partition.

-n_top_natives_to_optimize <Integer>

For use with the -optimize_decoy_discrimination flag. Objective function considers top N natives in partition function
Default: 1

Generate new structures in each round of iterative optE by repacking and minimizing the input decoys & natives using the weights obtained in the last round

-repack_and_minimize_input_structures <Boolean>

Minimizing the input decoys & natives using the starting weights – allows structures a chance to see the energy function before decoy discrimination begins without the memory overhead of the repack_and_minimize_decoys flag

-output_top_n_new_decoys <Integer>

For use with repack_and_minimize_decoys flag: Write out the top N decoys generated each round in this iterative refinement
Default: 0

-optimize_ligand_discrimination <File>

With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.

Turn the pssm probability vectors into unit vectors so that dot product is a true similarity measure

-min_decoy_rms_to_native <Real>

For use with the optimize_decoy_discrimination flag: exclude decoys that are within a certain RMS of the native structure

-max_rms_from_native <Real>

For use with the optimize_decoy_discrimination flag: exclude natives that are more than a certain RMS of the crystal structure. max_rms_from_native of 1.5, min_decoy_rms_from_native 2.0 would throw out structures in the range of 1.5 and 2.0 RMS from consideration

-optimize_starting_free_weights <Boolean>

With the iterative optE driver, try many different starting points for the minimization
Default: false

-wrap_dof_optimization <File>

Create new dofs and setup arithmetic dependencies for free dofs.

-randomly_perturb_starting_free_weights <Real>

With the iterative optE driver, perturb the weights by +/- <input value>=""> for those weights listed as free

-inv_kT_natrot <Real>

1 / kT for the pNativeRotamer fitness function
Default: 1

-inv_kT_nataa <Real>

1 / kT for the pNatAA and PSSM fitness function
Default: 1

-inv_kT_natstruct <Real>

1 / kT for the pNativeStructure fitness function
Default: 1

-mpi_weight_minimization <Boolean>

Distribute OptEMultifunc func/dfunc evaluations across nodes

-dont_use_reference_energies <Boolean>

Do not use reference energies anywhere during the protocol.
Default: false

-number_of_swarm_particles <Integer>

The number of particles to use during particle swarm weight optimization.
Default: 100

-number_of_swarm_cycles <Integer>

The number of cycles to run the swarm minimizer for.
Default: 20

-constrain_weights <File>

When minimizing the fitness objective function, also include weight constraints in the objective function

-fit_reference_energies_to_aa_profile_recovery <Boolean>

In the inner-loop sequence recovery/weight tweaking stage, accept/reject weight sets based on both the sequence recovery rate, and the mutual information between the expected and observed amino acid frequency distributions

-starting_refEs <File>

IterativeOptEDriver flag: specify a weights file to read reference energies from; do not optimize reference energies in the first round of weight fitting

-repeat_swarm_optimization_until_fitness_improves <Boolean>

After the first time though the particle swarm optimization phase, if the end fitness is not better than the start fitness, recreate the swarm around the start dofs and repeat the swarm optimization.
Default: false

-design_with_minpack <Boolean>

Use the min-packer to design during the sequence recovery stages.
Default: false

-design_with_fast_design <Boolean>

Use FastDesign to design during the sequence recovery stages.
Default: false

-design_with_offrotpack <Boolean>

Use the off-rotamer-packer to design during the sequence recovery stages.
Default: false

get the score for individual components in DARC scoring function
Default: false

-set_origin <Integer>

option to set orgin: 0 to choose origin based on R(rugedness) value, 1 for protein_center, 2 for eggshell_bottom, 3 for vector from eggshell_plane closest to protein_center, 4 for vector from eggshell_plane distant to protein_center, 5 for choosing a residue center as origin(use the flag -origin_res_num for choosing the residue number)
Default: 0

-origin_res_num <String>

Residue number:(optional)Chain to be used as origin for ray-casting
Default: "1"

Default number of repeats done by FastRelax. Has no effect if a custom script is used!
Default: 5

-dualspace <Boolean>

Do 3 FastRelax cycles of internal coordinate relax followed by two cycles of Cartesian relax - cart_bonded energy term is required, pro_close energy term should be turned off, and use of -relax::minimize_bond_angles is recommended. Use of the -nonideal flag switches all these and sets up correct min cycles, minimizer type, etc.

If true, positions for which the movemap prevents sidechain minimization will also have packing disabled. False by default.
Default: false

-bb_move <Boolean>

allow backbone to move during relax
Default: true

-chi_move <Boolean>

allow sidechain to move during relax
Default: true

-jump_move <Boolean>

allow jump to move during relax
Default: false

-dna_move <Boolean>

allow dna to move during relax + allow DNA-DNA interactions. Best if used with orbitals scorefunction. DNA stays together with great molprobity results. Not recommended for general use at this time.
Default: false

-fix_omega <Boolean>

Fix omega angles during relax
Default: false

-minimize_bond_lengths <Boolean>

Free bond length DOFs during relax for all atoms
Default: false

-minimize_bond_angles <Boolean>

Free bond angle DOFs during relax for all atoms
Default: false

-minimize_bondlength_subset <Integer>

Minimize only a subset of bondlengths 0 Default all bondlengths 1 backbone only 2 sidechain only 3 CA only (Ca-C,Ca-N and Ca-Cb)
Default: 0

-minimize_bondangle_subset <Integer>

Minimize only a subset of bondlengths 0 Default all bondangles 1 backbone only 2 sidechain only 3 tau only 4 Ca-Cb only
Default: 0

When picking fragments, fuzz fragments with multiple samples with Gaussians of this standard deviation
Default: 0

-rna_lores_chainbreak_weight <Real>

chainbreak weight for lo res sampling
Default: 0.0

-rna_lores_linear_chainbreak_weight <Real>

linear chainbreak weight for lo res sampling
Default: 0.0

-fixed_stems <Boolean>

Seed each stem with a Watson-Crick base pair instead of having the strands find each other
Default: false

-allow_bulge <Boolean>

Automatically virtualize residues that are not energetically stable
Default: false

-allowed_bulge_res <IntegerVector>

Use with allow_bulge, allowable pos for virtualization
Default: []

-allow_consecutive_bulges <Boolean>

allow_consecutive_bulges
Default: false

-move_first_rigid_body <Boolean>

first_rigid_body is usually kept frozen, but might be useful to sample it.
Default: false

-root_at_first_rigid_body <Boolean>

places coordinate system away from the usual last virtual residue and puts it on the first rigid body. useful if this rigidbody needs to be fixed, but other bodies need to move as if this one is moving. Use with -move_first_rigid_body.
Default: false

-dock_each_chunk <Boolean>

Dock each chunk, set fold tree up so that there are jumps from root virtual residue to all chunks, very useful for optimizing positions in density, use with -new_fold_tree_initializer
Default: true

-dock_each_chunk_per_chain <Boolean>

Dock each chunk, including multiple chunks from the same chain, set fold tree up so that there are jumps from root virtual residue to all chunks, very useful for optimizing positions in density, use with -dock_each_chunk and -new_fold_tree_initializer, may also want to use with -initial_structures
Default: false

-dock_chunks <FileVector>

Chunks that should be explicitly docked (the fold tree will be set up so that there are jumps from the root virtual residue to each of these chunks), use with -new_fold_tree_initializer
Default: "true"

-center_jumps_in_single_stranded <Boolean>

For RNA chains that don't have any base pairs, set up jumps in the center rather than at the first residue in the chain, use with -new_fold_tree_initializer and -dock_each_chunk
Default: false

Default is true (but it's only used if -initial_structures is also specified). May set to false with -initial_structures and either -dock_each_chunk_per_chain or -dock_chunks (and then you must include all concantenated sub-chunks from -initial_structures).
Default: true

-helical_substructs <FileVector>

Files provided with -s or -in:file:silent that represent helices, use with dock_each_chunk_per_chain and -new_fold_tree_initializer, includes moves that rotate and translate these helices along their helical axis
Default: ""

-suppress_bp_constraint <Real>

Factor by which to lower base pair constraint weight.
Default: 1.0

-output_filters <Boolean>

output lores scores at early stage (round 2 of 10) and at end – could be useable for early termination of unpromising early starts
Default: false